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From: Takeru KAMEDA (kamedapon_at_hiroshima-u.ac.jp)
Date: Tue May 28 2019 - 09:51:24 CDT

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Previous message: Peter Freddolino: "Re: Re: psfgen problems of many segment complex"
Maybe in reply to: Joao Ribeiro: "Re: Re: psfgen problems of many segment complex"
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Dear Peter

Thank you for your advising.

I tried in the structure excluding chain a :
=========================================================
......
......
......
psfgen) reading coordinates from pdb file psfgen_formatted_autopsf-temp.pdb_ZP1.pdb for segment ZP1
psfgen) Warning: failed to set coordinate for atom O THR:105 ZP1
segfiles psfgen_formatted_autopsf-temp.pdb_BP1.pdb psfgen_formatted_autopsf-temp.pdb_CP1.pdb psfgen_formatted_autopsf-temp.pdb_DP1.pdb psfgen_formatted_autopsf-temp.pdb_EP1.pdb psfgen_formatted_autopsf-temp.pdb_FP1.pdb psfgen_formatted_autopsf-temp.pdb_GP1.pdb psfgen_formatted_autopsf-temp.pdb_HP1.pdb psfgen_formatted_autopsf-temp.pdb_IP1.pdb psfgen_formatted_autopsf-temp.pdb_IP2.pdb psfgen_formatted_autopsf-temp.pdb_JP1.pdb psfgen_formatted_autopsf-temp.pdb_KP1.pdb psfgen_formatted_autopsf-temp.pdb_LP1.pdb psfgen_formatted_autopsf-temp.pdb_MP1.pdb psfgen_formatted_autopsf-temp.pdb_MP2.pdb psfgen_formatted_autopsf-temp.pdb_NP1.pdb psfgen_formatted_autopsf-temp.pdb_OP1.pdb psfgen_formatted_autopsf-temp.pdb_PP1.pdb psfgen_formatted_autopsf-temp.pdb_QP1.pdb psfgen_formatted_autopsf-temp.pdb_RP1.pdb psfgen_formatted_autopsf-temp.pdb_RP2.pdb psfgen_formatted_autopsf-temp.pdb_SP1.pdb psfgen_formatted_autopsf-temp.pdb_TP1.pdb psfgen_formatted_autopsf-temp.pdb_UP1.pdb psfgen_formatted_autopsf-temp.pdb_VP1.pdb psfgen
_formatted_autopsf-temp.pdb_WP1.pdb psfgen_formatted_autopsf-temp.pdb_XP1.pdb psfgen_formatted_autopsf-temp.pdb_YP1.pdb psfgen_formatted_autopsf-temp.pdb_ZP1.pdb psfgen_formatted_autopsf-temp.pdb_aP1.pdb psfgen_formatted_autopsf-temp.pdb_bP1.pdb psfgen_formatted_autopsf-temp.pdb_cP1.pdb psfgen_formatted_autopsf-temp.pdb_dP1.pdb psfgen_formatted_autopsf-temp.pdb_eP1.pdb psfgen_formatted_autopsf-temp.pdb_fP1.pdb psfgen_formatted_autopsf-temp.pdb_gP1.pdb psfgen_formatted_autopsf-temp.pdb_gP2.pdb psfgen_formatted_autopsf-temp.pdb_gP3.pdb psfgen_formatted_autopsf-temp.pdb_hP1.pdb psfgen_formatted_autopsf-temp.pdb_iP1.pdb psfgen_formatted_autopsf-temp.pdb_jP1.pdb psfgen_formatted_autopsf-temp.pdb_jP2.pdb psfgen_formatted_autopsf-temp.pdb_jP3.pdb psfgen_formatted_autopsf-temp.pdb_kP1.pdb psfgen_formatted_autopsf-temp.pdb_kP2.pdb psfgen_formatted_autopsf-temp.pdb_kP3.pdb psfgen_formatted_autopsf-temp.pdb_kP4.pdb psfgen_formatted_autopsf-temp.pdb_kP5.pdb psfgen_formatted_autopsf-temp.pdb_kP6.pdb psfgen_formatt!
ed_autop
s
f-temp.pdb_kP7.pdb psfgen_formatted_autopsf-temp.pdb_kP8.pdb psfgen_formatted_autopsf-temp.pdb_lP1.pdb psfgen_formatted_autopsf-temp.pdb_mP1.pdb psfgen_formatted_autopsf-temp.pdb_1N1.pdb psfgen_formatted_autopsf-temp.pdb_2N1.pdb psfgen_formatted_autopsf-temp.pdb_2N2.pdb psfgen_formatted_autopsf-temp.pdb_3N1.pdb
psfgen_formatted_autopsf-temp.pdb_aP1.pdb
30719 31488
psfgen) building segment aP1
psfgen) reading residues from pdb file psfgen_formatted_autopsf-temp.pdb_aP1.pdb
psfgen) extracted 97 residues from pdb file
psfgen) setting patch for first residue to PROP
psfgen) setting patch for last residue to CTER
psfgen) Info: generating structure...psfgen) Info: skipping improper N-C-CA-CD at beginning of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment.
psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
psfgen) Info: skipping conformation C-CA-N-CD at beginning of segment.
psfgen) Info: skipping bond C-N at end of segment.
psfgen) Info: skipping improper C-CA-N-O at end of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at end of segment.
psfgen) Info: skipping conformation CA-C-N-CA at end of segment.
psfgen) Info: skipping conformation N-CA-C-O at end of segment.
psfgen) Info: skipping conformation N-CA-C-N at end of segment.
aP1:98
aP1:2
segment complete.
psfgen) reading coordinates from pdb file psfgen_formatted_autopsf-temp.pdb_aP1.pdb for segment aP1
psfgen) Warning: failed to set coordinate for atom O PRO:98 aP1
segfiles psfgen_formatted_autopsf-temp.pdb_BP1.pdb psfgen_formatted_autopsf-temp.pdb_CP1.pdb psfgen_formatted_autopsf-temp.pdb_DP1.pdb psfgen_formatted_autopsf-temp.pdb_EP1.pdb psfgen_formatted_autopsf-temp.pdb_FP1.pdb psfgen_formatted_autopsf-temp.pdb_GP1.pdb psfgen_formatted_autopsf-temp.pdb_HP1.pdb psfgen_formatted_autopsf-temp.pdb_IP1.pdb psfgen_formatted_autopsf-temp.pdb_IP2.pdb psfgen_formatted_autopsf-temp.pdb_JP1.pdb psfgen_formatted_autopsf-temp.pdb_KP1.pdb psfgen_formatted_autopsf-temp.pdb_LP1.pdb psfgen_formatted_autopsf-temp.pdb_MP1.pdb psfgen_formatted_autopsf-temp.pdb_MP2.pdb psfgen_formatted_autopsf-temp.pdb_NP1.pdb psfgen_formatted_autopsf-temp.pdb_OP1.pdb psfgen_formatted_autopsf-temp.pdb_PP1.pdb psfgen_formatted_autopsf-temp.pdb_QP1.pdb psfgen_formatted_autopsf-temp.pdb_RP1.pdb psfgen_formatted_autopsf-temp.pdb_RP2.pdb psfgen_formatted_autopsf-temp.pdb_SP1.pdb psfgen_formatted_autopsf-temp.pdb_TP1.pdb psfgen_formatted_autopsf-temp.pdb_UP1.pdb psfgen_formatted_autopsf-temp.pdb_VP1.pdb psfgen
_formatted_autopsf-temp.pdb_WP1.pdb psfgen_formatted_autopsf-temp.pdb_XP1.pdb psfgen_formatted_autopsf-temp.pdb_YP1.pdb psfgen_formatted_autopsf-temp.pdb_ZP1.pdb psfgen_formatted_autopsf-temp.pdb_aP1.pdb psfgen_formatted_autopsf-temp.pdb_bP1.pdb psfgen_formatted_autopsf-temp.pdb_cP1.pdb psfgen_formatted_autopsf-temp.pdb_dP1.pdb psfgen_formatted_autopsf-temp.pdb_eP1.pdb psfgen_formatted_autopsf-temp.pdb_fP1.pdb psfgen_formatted_autopsf-temp.pdb_gP1.pdb psfgen_formatted_autopsf-temp.pdb_gP2.pdb psfgen_formatted_autopsf-temp.pdb_gP3.pdb psfgen_formatted_autopsf-temp.pdb_hP1.pdb psfgen_formatted_autopsf-temp.pdb_iP1.pdb psfgen_formatted_autopsf-temp.pdb_jP1.pdb psfgen_formatted_autopsf-temp.pdb_jP2.pdb psfgen_formatted_autopsf-temp.pdb_jP3.pdb psfgen_formatted_autopsf-temp.pdb_kP1.pdb psfgen_formatted_autopsf-temp.pdb_kP2.pdb psfgen_formatted_autopsf-temp.pdb_kP3.pdb psfgen_formatted_autopsf-temp.pdb_kP4.pdb psfgen_formatted_autopsf-temp.pdb_kP5.pdb psfgen_formatted_autopsf-temp.pdb_kP6.pdb psfgen_formatt!
ed_autop
s
f-temp.pdb_kP7.pdb psfgen_formatted_autopsf-temp.pdb_kP8.pdb psfgen_formatted_autopsf-temp.pdb_lP1.pdb psfgen_formatted_autopsf-temp.pdb_mP1.pdb psfgen_formatted_autopsf-temp.pdb_1N1.pdb psfgen_formatted_autopsf-temp.pdb_2N1.pdb psfgen_formatted_autopsf-temp.pdb_2N2.pdb psfgen_formatted_autopsf-temp.pdb_3N1.pdb
psfgen_formatted_autopsf-temp.pdb_bP1.pdb
31489 32097
psfgen) building segment bP1
Info) Coordinate I/O rate 0.25 frames/sec, 0 MB/sec, 4.0 sec
Info) Finished with coordinate file psfgen_formatted.pdb.
ERROR: Unable to open pdb file psfgen_formatted_autopsf-temp.pdb_bP1.pdb to read residues
=========================================================

Then, I tried in the structure excluding chain A :
=========================================================
......
......
......
psfgen) reading coordinates from pdb file psfgen_formatted_autopsf-temp.pdb_ZP1.pdb for segment ZP1
psfgen) Warning: failed to set coordinate for atom O THR:105 ZP1
segfiles psfgen_formatted_autopsf-temp.pdb_BP1.pdb psfgen_formatted_autopsf-temp.pdb_CP1.pdb psfgen_formatted_autopsf-temp.pdb_DP1.pdb psfgen_formatted_autopsf-temp.pdb_EP1.pdb psfgen_formatted_autopsf-temp.pdb_FP1.pdb psfgen_formatted_autopsf-temp.pdb_GP1.pdb psfgen_formatted_autopsf-temp.pdb_HP1.pdb psfgen_formatted_autopsf-temp.pdb_IP1.pdb psfgen_formatted_autopsf-temp.pdb_IP2.pdb psfgen_formatted_autopsf-temp.pdb_JP1.pdb psfgen_formatted_autopsf-temp.pdb_KP1.pdb psfgen_formatted_autopsf-temp.pdb_LP1.pdb psfgen_formatted_autopsf-temp.pdb_MP1.pdb psfgen_formatted_autopsf-temp.pdb_MP2.pdb psfgen_formatted_autopsf-temp.pdb_NP1.pdb psfgen_formatted_autopsf-temp.pdb_OP1.pdb psfgen_formatted_autopsf-temp.pdb_PP1.pdb psfgen_formatted_autopsf-temp.pdb_QP1.pdb psfgen_formatted_autopsf-temp.pdb_RP1.pdb psfgen_formatted_autopsf-temp.pdb_RP2.pdb psfgen_formatted_autopsf-temp.pdb_SP1.pdb psfgen_formatted_autopsf-temp.pdb_TP1.pdb psfgen_formatted_autopsf-temp.pdb_UP1.pdb psfgen_formatted_autopsf-temp.pdb_VP1.pdb psfgen
_formatted_autopsf-temp.pdb_WP1.pdb psfgen_formatted_autopsf-temp.pdb_XP1.pdb psfgen_formatted_autopsf-temp.pdb_YP1.pdb psfgen_formatted_autopsf-temp.pdb_ZP1.pdb psfgen_formatted_autopsf-temp.pdb_aP1.pdb psfgen_formatted_autopsf-temp.pdb_bP1.pdb psfgen_formatted_autopsf-temp.pdb_cP1.pdb psfgen_formatted_autopsf-temp.pdb_dP1.pdb psfgen_formatted_autopsf-temp.pdb_eP1.pdb psfgen_formatted_autopsf-temp.pdb_fP1.pdb psfgen_formatted_autopsf-temp.pdb_gP1.pdb psfgen_formatted_autopsf-temp.pdb_gP2.pdb psfgen_formatted_autopsf-temp.pdb_gP3.pdb psfgen_formatted_autopsf-temp.pdb_hP1.pdb psfgen_formatted_autopsf-temp.pdb_iP1.pdb psfgen_formatted_autopsf-temp.pdb_jP1.pdb psfgen_formatted_autopsf-temp.pdb_jP2.pdb psfgen_formatted_autopsf-temp.pdb_jP3.pdb psfgen_formatted_autopsf-temp.pdb_kP1.pdb psfgen_formatted_autopsf-temp.pdb_kP2.pdb psfgen_formatted_autopsf-temp.pdb_kP3.pdb psfgen_formatted_autopsf-temp.pdb_kP4.pdb psfgen_formatted_autopsf-temp.pdb_kP5.pdb psfgen_formatted_autopsf-temp.pdb_kP6.pdb psfgen_formatt!
ed_autop
s
f-temp.pdb_kP7.pdb psfgen_formatted_autopsf-temp.pdb_kP8.pdb psfgen_formatted_autopsf-temp.pdb_lP1.pdb psfgen_formatted_autopsf-temp.pdb_mP1.pdb psfgen_formatted_autopsf-temp.pdb_1N1.pdb psfgen_formatted_autopsf-temp.pdb_2N1.pdb psfgen_formatted_autopsf-temp.pdb_2N2.pdb psfgen_formatted_autopsf-temp.pdb_3N1.pdb
psfgen_formatted_autopsf-temp.pdb_aP1.pdb
30719 31488
psfgen) building segment aP1
psfgen) reading residues from pdb file psfgen_formatted_autopsf-temp.pdb_aP1.pdb
psfgen) extracted 97 residues from pdb file
psfgen) setting patch for first residue to PROP
psfgen) setting patch for last residue to CTER
psfgen) Info: generating structure...psfgen) Info: skipping improper N-C-CA-CD at beginning of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment.
psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
psfgen) Info: skipping conformation C-CA-N-CD at beginning of segment.
psfgen) Info: skipping bond C-N at end of segment.
psfgen) Info: skipping improper C-CA-N-O at end of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at end of segment.
psfgen) Info: skipping conformation CA-C-N-CA at end of segment.
psfgen) Info: skipping conformation N-CA-C-O at end of segment.
psfgen) Info: skipping conformation N-CA-C-N at end of segment.
aP1:98
aP1:2
segment complete.
psfgen) reading coordinates from pdb file psfgen_formatted_autopsf-temp.pdb_aP1.pdb for segment aP1
psfgen) Warning: failed to set coordinate for atom O PRO:98 aP1
segfiles psfgen_formatted_autopsf-temp.pdb_BP1.pdb psfgen_formatted_autopsf-temp.pdb_CP1.pdb psfgen_formatted_autopsf-temp.pdb_DP1.pdb psfgen_formatted_autopsf-temp.pdb_EP1.pdb psfgen_formatted_autopsf-temp.pdb_FP1.pdb psfgen_formatted_autopsf-temp.pdb_GP1.pdb psfgen_formatted_autopsf-temp.pdb_HP1.pdb psfgen_formatted_autopsf-temp.pdb_IP1.pdb psfgen_formatted_autopsf-temp.pdb_IP2.pdb psfgen_formatted_autopsf-temp.pdb_JP1.pdb psfgen_formatted_autopsf-temp.pdb_KP1.pdb psfgen_formatted_autopsf-temp.pdb_LP1.pdb psfgen_formatted_autopsf-temp.pdb_MP1.pdb psfgen_formatted_autopsf-temp.pdb_MP2.pdb psfgen_formatted_autopsf-temp.pdb_NP1.pdb psfgen_formatted_autopsf-temp.pdb_OP1.pdb psfgen_formatted_autopsf-temp.pdb_PP1.pdb psfgen_formatted_autopsf-temp.pdb_QP1.pdb psfgen_formatted_autopsf-temp.pdb_RP1.pdb psfgen_formatted_autopsf-temp.pdb_RP2.pdb psfgen_formatted_autopsf-temp.pdb_SP1.pdb psfgen_formatted_autopsf-temp.pdb_TP1.pdb psfgen_formatted_autopsf-temp.pdb_UP1.pdb psfgen_formatted_autopsf-temp.pdb_VP1.pdb psfgen
_formatted_autopsf-temp.pdb_WP1.pdb psfgen_formatted_autopsf-temp.pdb_XP1.pdb psfgen_formatted_autopsf-temp.pdb_YP1.pdb psfgen_formatted_autopsf-temp.pdb_ZP1.pdb psfgen_formatted_autopsf-temp.pdb_aP1.pdb psfgen_formatted_autopsf-temp.pdb_bP1.pdb psfgen_formatted_autopsf-temp.pdb_cP1.pdb psfgen_formatted_autopsf-temp.pdb_dP1.pdb psfgen_formatted_autopsf-temp.pdb_eP1.pdb psfgen_formatted_autopsf-temp.pdb_fP1.pdb psfgen_formatted_autopsf-temp.pdb_gP1.pdb psfgen_formatted_autopsf-temp.pdb_gP2.pdb psfgen_formatted_autopsf-temp.pdb_gP3.pdb psfgen_formatted_autopsf-temp.pdb_hP1.pdb psfgen_formatted_autopsf-temp.pdb_iP1.pdb psfgen_formatted_autopsf-temp.pdb_jP1.pdb psfgen_formatted_autopsf-temp.pdb_jP2.pdb psfgen_formatted_autopsf-temp.pdb_jP3.pdb psfgen_formatted_autopsf-temp.pdb_kP1.pdb psfgen_formatted_autopsf-temp.pdb_kP2.pdb psfgen_formatted_autopsf-temp.pdb_kP3.pdb psfgen_formatted_autopsf-temp.pdb_kP4.pdb psfgen_formatted_autopsf-temp.pdb_kP5.pdb psfgen_formatted_autopsf-temp.pdb_kP6.pdb psfgen_formatt!
ed_autop
s
f-temp.pdb_kP7.pdb psfgen_formatted_autopsf-temp.pdb_kP8.pdb psfgen_formatted_autopsf-temp.pdb_lP1.pdb psfgen_formatted_autopsf-temp.pdb_mP1.pdb psfgen_formatted_autopsf-temp.pdb_1N1.pdb psfgen_formatted_autopsf-temp.pdb_2N1.pdb psfgen_formatted_autopsf-temp.pdb_2N2.pdb psfgen_formatted_autopsf-temp.pdb_3N1.pdb
psfgen_formatted_autopsf-temp.pdb_bP1.pdb
31489 32097
psfgen) building segment bP1
Info) Coordinate I/O rate 0.22 frames/sec, 0 MB/sec, 4.5 sec
Info) Finished with coordinate file psfgen_formatted.pdb.
ERROR: Unable to open pdb file psfgen_formatted_autopsf-temp.pdb_bP1.pdb to read residues

MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
ERROR: failed while building segment
=========================================================

Each error occurs in proccessing chain b.

Overlapping (small) a and (large) A seems essential problem.

Thank you in advance.
    Best wishes,
    Takeru Kameda
    PhD Student, Hiroshima University, Japan

________________________________________
差出人: Peter Freddolino <petefred_at_umich.edu>
送信日時: 2019年5月28日 23:29
宛先: Takeru KAMEDA
CC: Joao Ribeiro; vmd-l_at_ks.uiuc.edu
件名: Re: vmd-l: Re: psfgen problems of many segment complex

Dear Takeru,
Given that chain a seems to be causing so many problems -- are you able to build the structure if you exclude chain 'a'? What if you try only chain 'a' and nothing else? What if you exclude chain 'A'?
Thanks,
Peter

On Tue, May 28, 2019 at 10:16 AM Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>> wrote:
Dear João
Thank you for your advising.

(And, I'm sorry I sent the same email twice. I don't remember I sent it ... )

I tried your recommended command, following message were shown :
========================================================
.....
.....
.....

psfgen) reading coordinates from pdb file psfgen_formatted_autopsf-temp.pdb_YP1.pdb for segment YP1
psfgen) Warning: failed to set coordinate for atom O ASP:135 YP1
segfiles psfgen_formatted_autopsf-temp.pdb_AP1.pdb psfgen_formatted_autopsf-temp.pdb_BP1.pdb psfgen_formatted_autopsf-temp.pdb_CP1.pdb psfgen_formatted_autopsf-temp.pdb_DP1.pdb psfgen_formatted_autopsf-temp.pdb_EP1.pdb psfgen_formatted_autopsf-temp.pdb_FP1.pdb psfgen_formatted_autopsf-temp.pdb_GP1.pdb psfgen_formatted_autopsf-temp.pdb_HP1.pdb psfgen_formatted_autopsf-temp.pdb_IP1.pdb psfgen_formatted_autopsf-temp.pdb_IP2.pdb psfgen_formatted_autopsf-temp.pdb_JP1.pdb psfgen_formatted_autopsf-temp.pdb_KP1.pdb psfgen_formatted_autopsf-temp.pdb_LP1.pdb psfgen_formatted_autopsf-temp.pdb_MP1.pdb psfgen_formatted_autopsf-temp.pdb_MP2.pdb psfgen_formatted_autopsf-temp.pdb_NP1.pdb psfgen_formatted_autopsf-temp.pdb_OP1.pdb psfgen_formatted_autopsf-temp.pdb_PP1.pdb psfgen_formatted_autopsf-temp.pdb_QP1.pdb psfgen_formatted_autopsf-temp.pdb_RP1.pdb psfgen_formatted_autopsf-temp.pdb_RP2.pdb psfgen_formatted_autopsf-temp.pdb_SP1.pdb psfgen_formatted_autopsf-temp.pdb_TP1.pdb psfgen_formatted_autopsf-temp.pdb_UP1.pdb psfgen
_formatted_autopsf-temp.pdb_VP1.pdb psfgen_formatted_autopsf-temp.pdb_WP1.pdb psfgen_formatted_autopsf-temp.pdb_XP1.pdb psfgen_formatted_autopsf-temp.pdb_YP1.pdb psfgen_formatted_autopsf-temp.pdb_ZP1.pdb psfgen_formatted_autopsf-temp.pdb_aP1.pdb psfgen_formatted_autopsf-temp.pdb_bP1.pdb psfgen_formatted_autopsf-temp.pdb_cP1.pdb psfgen_formatted_autopsf-temp.pdb_dP1.pdb psfgen_formatted_autopsf-temp.pdb_eP1.pdb psfgen_formatted_autopsf-temp.pdb_fP1.pdb psfgen_formatted_autopsf-temp.pdb_gP1.pdb psfgen_formatted_autopsf-temp.pdb_gP2.pdb psfgen_formatted_autopsf-temp.pdb_gP3.pdb psfgen_formatted_autopsf-temp.pdb_hP1.pdb psfgen_formatted_autopsf-temp.pdb_iP1.pdb psfgen_formatted_autopsf-temp.pdb_jP1.pdb psfgen_formatted_autopsf-temp.pdb_jP2.pdb psfgen_formatted_autopsf-temp.pdb_jP3.pdb psfgen_formatted_autopsf-temp.pdb_kP1.pdb psfgen_formatted_autopsf-temp.pdb_kP2.pdb psfgen_formatted_autopsf-temp.pdb_kP3.pdb psfgen_formatted_autopsf-temp.pdb_kP4.pdb psfgen_formatted_autopsf-temp.pdb_kP5.pdb psfgen_formatt!
ed_autop
s
f-temp.pdb_kP6.pdb psfgen_formatted_autopsf-temp.pdb_kP7.pdb psfgen_formatted_autopsf-temp.pdb_kP8.pdb psfgen_formatted_autopsf-temp.pdb_lP1.pdb psfgen_formatted_autopsf-temp.pdb_mP1.pdb psfgen_formatted_autopsf-temp.pdb_1N1.pdb psfgen_formatted_autopsf-temp.pdb_2N1.pdb psfgen_formatted_autopsf-temp.pdb_2N2.pdb psfgen_formatted_autopsf-temp.pdb_3N1.pdb
psfgen_formatted_autopsf-temp.pdb_ZP1.pdb
31786 32343
psfgen) building segment ZP1
psfgen) reading residues from pdb file psfgen_formatted_autopsf-temp.pdb_ZP1.pdb
psfgen) extracted 70 residues from pdb file
psfgen) setting patch for first residue to NTER
psfgen) setting patch for last residue to CTER
psfgen) Info: generating structure...psfgen) Info: skipping improper N-C-CA-HN at beginning of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment.
psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment.
psfgen) Info: skipping bond C-N at end of segment.
psfgen) Info: skipping improper C-CA-N-O at end of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at end of segment.
psfgen) Info: skipping conformation CA-C-N-CA at end of segment.
psfgen) Info: skipping conformation N-CA-C-O at end of segment.
psfgen) Info: skipping conformation N-CA-C-N at end of segment.
ZP1:105
ZP1:36
segment complete.
psfgen) reading coordinates from pdb file psfgen_formatted_autopsf-temp.pdb_ZP1.pdb for segment ZP1
psfgen) Warning: failed to set coordinate for atom O THR:105 ZP1
segfiles psfgen_formatted_autopsf-temp.pdb_AP1.pdb psfgen_formatted_autopsf-temp.pdb_BP1.pdb psfgen_formatted_autopsf-temp.pdb_CP1.pdb psfgen_formatted_autopsf-temp.pdb_DP1.pdb psfgen_formatted_autopsf-temp.pdb_EP1.pdb psfgen_formatted_autopsf-temp.pdb_FP1.pdb psfgen_formatted_autopsf-temp.pdb_GP1.pdb psfgen_formatted_autopsf-temp.pdb_HP1.pdb psfgen_formatted_autopsf-temp.pdb_IP1.pdb psfgen_formatted_autopsf-temp.pdb_IP2.pdb psfgen_formatted_autopsf-temp.pdb_JP1.pdb psfgen_formatted_autopsf-temp.pdb_KP1.pdb psfgen_formatted_autopsf-temp.pdb_LP1.pdb psfgen_formatted_autopsf-temp.pdb_MP1.pdb psfgen_formatted_autopsf-temp.pdb_MP2.pdb psfgen_formatted_autopsf-temp.pdb_NP1.pdb psfgen_formatted_autopsf-temp.pdb_OP1.pdb psfgen_formatted_autopsf-temp.pdb_PP1.pdb psfgen_formatted_autopsf-temp.pdb_QP1.pdb psfgen_formatted_autopsf-temp.pdb_RP1.pdb psfgen_formatted_autopsf-temp.pdb_RP2.pdb psfgen_formatted_autopsf-temp.pdb_SP1.pdb psfgen_formatted_autopsf-temp.pdb_TP1.pdb psfgen_formatted_autopsf-temp.pdb_UP1.pdb psfgen
_formatted_autopsf-temp.pdb_VP1.pdb psfgen_formatted_autopsf-temp.pdb_WP1.pdb psfgen_formatted_autopsf-temp.pdb_XP1.pdb psfgen_formatted_autopsf-temp.pdb_YP1.pdb psfgen_formatted_autopsf-temp.pdb_ZP1.pdb psfgen_formatted_autopsf-temp.pdb_aP1.pdb psfgen_formatted_autopsf-temp.pdb_bP1.pdb psfgen_formatted_autopsf-temp.pdb_cP1.pdb psfgen_formatted_autopsf-temp.pdb_dP1.pdb psfgen_formatted_autopsf-temp.pdb_eP1.pdb psfgen_formatted_autopsf-temp.pdb_fP1.pdb psfgen_formatted_autopsf-temp.pdb_gP1.pdb psfgen_formatted_autopsf-temp.pdb_gP2.pdb psfgen_formatted_autopsf-temp.pdb_gP3.pdb psfgen_formatted_autopsf-temp.pdb_hP1.pdb psfgen_formatted_autopsf-temp.pdb_iP1.pdb psfgen_formatted_autopsf-temp.pdb_jP1.pdb psfgen_formatted_autopsf-temp.pdb_jP2.pdb psfgen_formatted_autopsf-temp.pdb_jP3.pdb psfgen_formatted_autopsf-temp.pdb_kP1.pdb psfgen_formatted_autopsf-temp.pdb_kP2.pdb psfgen_formatted_autopsf-temp.pdb_kP3.pdb psfgen_formatted_autopsf-temp.pdb_kP4.pdb psfgen_formatted_autopsf-temp.pdb_kP5.pdb psfgen_formatt!
ed_autop
s
f-temp.pdb_kP6.pdb psfgen_formatted_autopsf-temp.pdb_kP7.pdb psfgen_formatted_autopsf-temp.pdb_kP8.pdb psfgen_formatted_autopsf-temp.pdb_lP1.pdb psfgen_formatted_autopsf-temp.pdb_mP1.pdb psfgen_formatted_autopsf-temp.pdb_1N1.pdb psfgen_formatted_autopsf-temp.pdb_2N1.pdb psfgen_formatted_autopsf-temp.pdb_2N2.pdb psfgen_formatted_autopsf-temp.pdb_3N1.pdb
psfgen_formatted_autopsf-temp.pdb_aP1.pdb
32344 33113
psfgen) building segment aP1
Info) Coordinate I/O rate 0.20 frames/sec, 0 MB/sec, 5.1 sec
Info) Finished with coordinate file psfgen_formatted.pdb.
ERROR: Unable to open pdb file psfgen_formatted_autopsf-temp.pdb_aP1.pdb to read residues
========================================================

Such error occurs when the proccessing reachs to segment a (not A).
Previously, we performed usual psfgen, an error was shown in the case of segment a.
Thank you in advance.
    Best wishes,
    Takeru Kameda
    PhD Student, Hiroshima University, Japan

________________________________________
差出人: Joao Ribeiro <jribeiro_at_ks.uiuc.edu<mailto:jribeiro_at_ks.uiuc.edu>>
送信日時: 2019年5月28日 22:45
宛先: Takeru KAMEDA; Peter Freddolino
CC: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
件名: Re: vmd-l: Re: psfgen problems of many segment complex

Dear Takeru,

Please try :"autopsf -protein -nucleic -prefix psfgen -top [list ./../toppar/top_all36_na.rtf ./../toppar/top_all36_prot.rtf ./../toppar/top_all36_carb.rtf ./../toppar/top_all36_lipid.rtf]"

Basically, every time the -top flag, the list of topology files to be loaded is initialized.

Best

João

……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
https://jpn01.safelinks.protection.outlook.com/?url=http:%2F%2Fwww.ks.uiuc.edu%2F~jribeiro%2F&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Ca0a6985d6d19405f8cef08d6e372c028%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C636946479336972016&sdata=VXwlr5KboP9kTDjO42HY%2Byk3YM73Z33c4liPP219488%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http:%2F%2Fwww.ks.uiuc.edu%2F~jribeiro%2F&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C07e1d267eab54ed27a8b08d6e378e6f2%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C636946505763734625&sdata=DMOxLUz4BjNvBOjaWzR2oPZYgcMbKfVYw15aAkB1S1M%3D&reserved=0>
jribeiro_at_illinois.edu<mailto:jribeiro_at_illinois.edu>
+1 (217) 3005851

On 5/28/19, 8:28 AM, "Takeru KAMEDA" <owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> on behalf of kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>> wrote:

Dear Peter

Thank you for your advising.

We tried following command :

=========================================================
resetpsf

autopsf -protein -nucleic -prefix psfgen -top ./../toppar/top_all36_na.rtf -top ./../toppar/top_all36_prot.rtf -top ./../toppar/top_all36_carb.rtf -top ./../toppar/top_all36_lipid.rtf
=========================================================

and GUI interface.
However, following error was print :

    =========================================================
    segfiles psfgen_formatted_autopsf-temp.pdb_AP1.pdb psfgen_formatted_autopsf-temp.pdb_BP1.pdb psfgen_formatted_autopsf-temp.pdb_CP1.pdb psfgen_formatted_autopsf-temp.pdb_DP1.pdb psfgen_formatted_autopsf-temp.pdb_EP1.pdb psfgen_formatted_autopsf-temp.pdb_FP1.pdb psfgen_formatted_autopsf-temp.pdb_GP1.pdb psfgen_formatted_autopsf-temp.pdb_HP1.pdb psfgen_formatted_autopsf-temp.pdb_IP1.pdb psfgen_formatted_autopsf-temp.pdb_IP2.pdb psfgen_formatted_autopsf-temp.pdb_JP1.pdb psfgen_formatted_autopsf-temp.pdb_KP1.pdb psfgen_formatted_autopsf-temp.pdb_LP1.pdb psfgen_formatted_autopsf-temp.pdb_MP1.pdb psfgen_formatted_autopsf-temp.pdb_MP2.pdb psfgen_formatted_autopsf-temp.pdb_NP1.pdb psfgen_formatted_autopsf-temp.pdb_OP1.pdb psfgen_formatted_autopsf-temp.pdb_PP1.pdb psfgen_formatted_autopsf-temp.pdb_QP1.pdb psfgen_formatted_autopsf-temp.pdb_RP1.pdb psfgen_formatted_autopsf-temp.pdb_RP2.pdb psfgen_formatted_autopsf-temp.pdb_SP1.pdb psfgen_formatted_autopsf-temp.pdb_TP1.pdb psfgen_formatted_autopsf-temp.pdb_UP1.pdb ps
fgen_formatted_autopsf-temp.pdb_VP1.pdb psfgen_formatted_autopsf-temp.pdb_WP1.pdb psfgen_formatted_autopsf-temp.pdb_XP1.pdb psfgen_formatted_autopsf-temp.pdb_YP1.pdb psfgen_formatted_autopsf-temp.pdb_ZP1.pdb psfgen_formatted_autopsf-temp.pdb_aP1.pdb psfgen_formatted_autopsf-temp.pdb_bP1.pdb psfgen_formatted_autopsf-temp.pdb_cP1.pdb psfgen_formatted_autopsf-temp.pdb_dP1.pdb psfgen_formatted_autopsf-temp.pdb_eP1.pdb psfgen_formatted_autopsf-temp.pdb_fP1.pdb psfgen_formatted_autopsf-temp.pdb_gP1.pdb psfgen_formatted_autopsf-temp.pdb_gP2.pdb psfgen_formatted_autopsf-temp.pdb_gP3.pdb psfgen_formatted_autopsf-temp.pdb_hP1.pdb psfgen_formatted_autopsf-temp.pdb_iP1.pdb psfgen_formatted_autopsf-temp.pdb_jP1.pdb psfgen_formatted_autopsf-temp.pdb_jP2.pdb psfgen_formatted_autopsf-temp.pdb_jP3.pdb psfgen_formatted_autopsf-temp.pdb_kP1.pdb psfgen_formatted_autopsf-temp.pdb_kP2.pdb psfgen_formatted_autopsf-temp.pdb_kP3.pdb psfgen_formatted_autopsf-temp.pdb_kP4.pdb psfgen_formatted_autopsf-temp.pdb_kP5.pdb psfgen_for!
matt!
     ed_autop
    sf-temp.pdb_kP6.pdb psfgen_formatted_autopsf-temp.pdb_kP7.pdb psfgen_formatted_autopsf-temp.pdb_kP8.pdb psfgen_formatted_autopsf-temp.pdb_lP1.pdb psfgen_formatted_autopsf-temp.pdb_mP1.pdb psfgen_formatted_autopsf-temp.pdb_1N1.pdb psfgen_formatted_autopsf-temp.pdb_2N1.pdb psfgen_formatted_autopsf-temp.pdb_2N2.pdb psfgen_formatted_autopsf-temp.pdb_3N1.pdb
    psfgen_formatted_autopsf-temp.pdb_AP1.pdb
    1 1625
    psfgen) building segment AP1
    psfgen) reading residues from pdb file psfgen_formatted_autopsf-temp.pdb_AP1.pdb
    psfgen) extracted 97 residues from pdb file
    psfgen) setting patch for first residue to NTER
    psfgen) setting patch for last residue to CTER
    psfgen) Info: generating structure...psfgen) unknown patch type CTER
    failed!
    Info) Coordinate I/O rate 0.19 frames/sec, 0 MB/sec, 5.2 sec
    Info) Finished with coordinate file psfgen_formatted.pdb.
    ERROR: failed on end of segment
    MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
    =========================================================

Why such error was shown?

Any editing of PDB file are necessary ?

    Thank you in advance.
    Best wishes,
    Takeru Kameda
    PhD Student, Hiroshima University, Japan

    ________________________________________
    差出人: Peter Freddolino <petefred_at_umich.edu<mailto:petefred_at_umich.edu>>
    送信日時: 2019年5月27日 22:47
    宛先: Takeru KAMEDA
    CC: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
    件名: Re: psfgen problems of many segment complex

You do not need to give segment names that are the same as the chain names in the pdb -- in fact I would advise against it. Autopsf, for example, just calls protein chains P1, P2, etc.

Best,
Peter

On Fri, May 24, 2019 at 11:14 AM Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>>> wrote:
Dear VMD Users

    Takeru Kameda
    PhD Student, Hiroshima University, Japan
    The PSFgen script we used is as follows:

    """""""""""""""""""""""""""""""""""""""""""""""""
    package require psfgen
    resetpsf
    topology ./../toppar/top_all36_na.rtf
    topology ./../toppar/top_all36_prot.rtf
    topology ./../toppar/top_all36_carb.rtf
    topology ./../toppar/top_all36_cgenff.rtf
    topology ./../toppar/top_all36_lipid.rtf
    pdbalias residue A ADE
    pdbalias residue G GUA
    pdbalias residue C CYT
    pdbalias residue T THY
    pdbalias residue U URA
    pdbalias residue HIS HSE
    pdbalias atom ILE CD1 CD
    ## protein
    set sel [atomselect top protein]
    set chains [lsort -unique [$sel get chain]] ;# return A B C D
    foreach chain $chains {
        puts "Adding protein chain $chain to psfgen"
        set seg ${chain}PRO
        set sel [atomselect top "protein and chain $chain"]
        $sel set segid $seg
        $sel writepdb tmp.pdb
        segment $seg {
            #first NTER
            #last CTER
            pdb tmp.pdb
        }
        coordpdb tmp.pdb
    }
    ## RNA
    set sel [atomselect top nucleic]
    set chains [lsort -unique [$sel get chain]];# return A B C D
    foreach chain $chains {
        puts "Adding RNA chain $chain to psfgen"
        set seg ${chain}RNA
        set sel [atomselect top "nucleic and chain $chain"]
        $sel set segid $seg
        $sel writepdb tmp.pdb

segment $seg { pdb tmp.pdb }

        set resids [lsort -unique [$sel get resid]]
        #foreach r $resids {
        #patch DEOX $seg:$r
        #}
        regenerate angles dihedrals
        coordpdb tmp.pdb
    }
    guesscoord
    writepsf psfgen.psf
    writepdb psfgen.pdb
    """""""""""""""""""""""""""""""""""""""""""""""""
    --

    ________________________________
    差出人: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov><mailto:Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>>>
    送信日時: 2019年5月24日 21:52
    宛先: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu><mailto:vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>>; Takeru KAMEDA
    件名: RE: psfgen problems of many segment complex

One segment at a time would be my advice. That's how the psfgen user guide does it (see page 4, where the protein BPTI is in a different segment than the water).

-Josh

On 2019-05-24 00:56:17-06:00 owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu><mailto:owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>> wrote:

Dear VMD Users

I have a question about how to apply psfgen to a complex with many segments

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