Re: PSFGEN

From: Hyun Chul Lee (lee252_at_purdue.edu)
Date: Thu Dec 10 2009 - 22:27:04 CST

Here is the links of files.
http://web.ics.purdue.edu/~lee252/test.pdb
http://web.ics.purdue.edu/~lee252/test.tcl
http://web.ics.purdue.edu/~lee252/top_all22_prot_add.inp

Hyun Chul Lee,

--------------------------------------------------
From: "Hyun Chul Lee" <lee252_at_purdue.edu>
Sent: Monday, December 07, 2009 4:36 PM
To: "namd-l" <namd-l_at_ks.uiuc.edu>
Subject: PSFGEN

> I sent a question last week, but it wasn't posted.
> I'm just a beginner in MD simulation. So I would appreciate if someone
> help me to solve my problem.
>
> -------------------------------------------------
> Here is my question
>
> I'm working on generating ensemble structures of gold cluster labled
> proteins,
> so added new residue which is called UDG in topology file and parameter
> files.
>
> But when I run initial NAMD test I got ""FATAL ERROR: Multiplicity of
> Paramters for diehedral bond ..." errors.
> As far as I figure out, this error came from generating PSF file using
> PSFGEN program with user defined residue (UDG).
> I deleted all atoms except one in UDG, and run NAMD test. But I still got
> same results.
>
> --------------------
> The followings are simple examples (three amino acids plus dummy atom)
> which cause the same problem that I got in the gold cluster labeled
> proteins.
>
> -----------------------------------------------
> #"test.pdb"
> ATOM 1 N MET 1 53.882 -29.488 26.600 1.00 89.87
> N
> ATOM 2 CA MET 1 53.358 -28.278 25.877 1.00 90.31
> C
> ATOM 3 C MET 1 52.040 -28.493 25.123 1.00 91.07
> C
> ATOM 4 O MET 1 51.729 -29.610 24.666 1.00 93.30
> O
> ATOM 5 CB MET 1 54.436 -27.705 24.979 1.00 89.16
> C
> ATOM 6 CG MET 1 55.603 -27.244 25.797 1.00 89.35
> C
> ATOM 7 SD MET 1 56.229 -25.716 25.169 1.00 95.74
> S
> ATOM 8 CE MET 1 54.709 -24.639 25.257 1.00 94.48
> C
> ATOM 9 N GLU 2 51.298 -27.410 24.920 1.00 88.09
> N
> ATOM 10 CA GLU 2 49.982 -27.550 24.320 1.00 86.65
> C
> ATOM 11 C GLU 2 49.471 -26.556 23.297 1.00 83.87
> C
> ATOM 12 O GLU 2 50.143 -25.595 22.920 1.00 84.96
> O
> ATOM 13 CB GLU 2 48.972 -27.547 25.448 1.00 88.26
> C
> ATOM 14 CG GLU 2 49.000 -28.761 26.276 1.00 92.09
> C
> ATOM 15 CD GLU 2 47.624 -29.239 26.490 1.00 94.28
> C
> ATOM 16 OE1 GLU 2 47.137 -29.961 25.589 1.00 93.09
> O
> ATOM 17 OE2 GLU 2 47.038 -28.848 27.527 1.00 97.38
> O1-
> ATOM 18 N GLY 3 48.185 -26.729 22.984 1.00 78.60
> N
> ATOM 19 CA GLY 3 47.486 -25.845 22.085 1.00 68.74
> C
> ATOM 20 C GLY 3 47.227 -24.542 22.809 1.00 64.86
> C
> ATOM 21 O GLY 3 46.260 -23.852 22.518 1.00 62.22
> O
> ATOM 22 DUM UDG 4 47.932 -23.012 24.554 1.00 59.24
> DUM
>
> -----------------------------------------------
> #newly added lines in "top_all22_prot_add.inp"
> !For test [Here_to_edit]
> RESI UDG 0.00
> GROUP
> ATOM DUM DUM 0.00
>
> PRES UDGL 0.00 ! patch for GLY-DUM [Here_to_edit]
> ATOM C C 0.00
> ATOM DUM DUM 0.00
> BOND C DUM
>
> ---------------------------------------
> #test.tcl
> # Create working directory; remove old output files
> mkdir -p output
> rm -f output/*
>
> #(2) Embed the psfgen commands in this script
> psfgen << ENDMOL
>
> #(3) Read topology file
> topology top_all22_prot_add.inp
>
> #(4) Build protein segment
> segment UDGP {
> pdb test.pdb
> }
>
> #(5) Patch protein to UDG
> patch UDGL UDGP:3 UDGP:4
>
> #(6) Read protein coordinates from PDB files
> coordpdb test.pdb UDGP
>
> #(9) Guess missing coordinates
> guesscoord
>
> #(10) Write structure and coordinate files
> writepsf output/test_namd.psf
> writepdb output/test_namd.pdb
>
> ----------------------------------------------
> $ ./test.tcl
>
> PSFGEN from NAMD 2.7b1 for MacOSX-x86
> reading topology file top_all22_prot_add.inp
>
>>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
>>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
>>>>>>>>>>>>>>>>>>>>>>> December, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
> All comments to ADM jr. via the CHARMM web site: www.charmm.org
> parameter set discussion forum
>
> Created by CHARMM version 31 1
> cross-term entries present in topology definitions
> building segment UDGP
> reading residues from pdb file test.pdb
> extracted 4 residues from pdb file
> Info: generating structure...
> Info: skipping improper N-C-CA-HN at beginning of segment.
> Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment.
> Info: skipping conformation C-N-CA-C at beginning of segment.
> Info: skipping conformation C-CA-N-HN at beginning of segment.
> ERROR: Missing atoms for bond C(0) N(1) in residue GLY:3
> ERROR: Missing atoms for improper C(0) CA(0) N(1) O(0)
> in residue GLY:3
> ERROR: Missing atoms for cross-term C(-1) N(0) CA(0) C(0) N(0) CA(0) C(0)
> N(1)
> in residue GLY:3
> Missing atoms for conformation definition
> Missing atoms for conformation definition
> Missing atoms for conformation definition
> UDGP:1
> Info: segment complete.
> applying patch UDGL to 2 residues
> UDGP:3 UDGP:4
> reading coordinates from pdb file test.pdb for segment UDGP
> Info: guessing coordinates for 21 atoms (0 non-hydrogen)
> Warning: poorly guessed coordinates for 4 atoms (0 non-hydrogen):
> Warning: poorly guessed coordinate for atom HT1 MET:1 UDGP
> Warning: poorly guessed coordinate for atom HT2 MET:1 UDGP
> Warning: poorly guessed coordinate for atom HT3 MET:1 UDGP
> Warning: poorly guessed coordinate for atom DUM GLY:3 UDGP
> Info: writing psf file output/test_namd.psf
> total of 43 atoms
> total of 41 bonds
> total of 71 angles
> total of 92 dihedrals
> total of 5 impropers
> total of 1 cross-terms
> Info: psf file complete.
> Info: writing pdb file output/test_namd.pdb
> Info: Atoms with guessed coordinates will have occupancy of 0.0.
> Info: pdb file complete.
> ------------------------------------------------------------------
>
> There could be a mistake in patching residue.
> But I don't think this is the reason causing this error.
>
> If anyone who knows how to debug this error, please let me know.
>
> Thanks,
> Hyun Chul Lee,

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