VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue May 28 2019 - 10:05:05 CDT

Could you please send me your input pdb file (off-list) or pdb code for
what you're working with?
Thanks,
Peter

On Tue, May 28, 2019 at 10:58 AM Takeru KAMEDA <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_formatt!
> ed_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_kP!
> 4.pdb psfgen_formatted_autopsf-temp.pdb_kP5.pdb psfgen_formatt!
> 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>
> 送信日時: 2019年5月27日 22:47
> 宛先: Takeru KAMEDA
> CC: 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>> wrote:
> Dear VMD Users
>
> Somehow my previous mail was not sent to the end (Sorry).
> I have a question about how to apply psfgen to a complex with many
> segments.
> We tried to use the structure (PDB: 3J81) with many segments (chains) as
> follows.
> A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k
> l m 1 2 3
> (https://www.rcsb.org/structure/3j81<
> https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rcsb.org%2Fstructure%2F3j81&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C811e782749d945b9b66c08d6e2a9d78b%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C636945616433999940&sdata=R6X%2BZ4oNjCR5HH%2BebBb7GvLmhiac225ayiRvTrXXO84%3D&reserved=0
> >)
> However, we could not finish the psfgen script.
> It seems that chain ID is case insensitive and hence e.g. chains A and a
> are regarded as duplicated chain IDs.
> Could you tell me how to solve the problem?
> We employed VMD 1.9.3 (psfgen version1.6.4), and CHARMM36 parameter. (
> http://mackerell.umaryland.edu/charmm_ff.shtml<
> https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmackerell.umaryland.edu%2Fcharmm_ff.shtml&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C811e782749d945b9b66c08d6e2a9d78b%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C636945616434009934&sdata=wFXSZtV0nhA%2F%2FWuvUJviNV%2B0gXwWKuZtTY5JwD3%2FHR4%3D&reserved=0
> >)
> Thank you in advance.
> Best wishes,
>
> 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>>
> 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>; 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> wrote:
>
> Dear VMD Users
>
> I have a question about how to apply psfgen to a complex with many segments
>
>