Re: psfgen fails to set coords for all atoms

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 27 2009 - 15:56:05 CST

On Fri, 2009-11-27 at 14:06 -0700, Blake Mertz wrote:

hi blake,

> I'm running into a problem with my setup for MD testing of a molecule
> fragment against some QM results that I've compiled. My situation is
> this: I've got my fragment and want to do a dihedral scan of a methyl
> group. The appropriate fixed atoms are prepped with their values in
> the occupancy field, and all of my atoms are in the intial positions I
> want them, so I really don't need psfgen to guess their coordinates.

if you don't need it, don't specify the guesscoord command.

> I've spent the last couple weeks trying to find some answers on
> namd-l, but haven't really run across anyone with the specific error
> "Warning: failed to set coordinate" for every atom in their molecule.
> Here are some short examples from my files, starting with the psfgen

strange. i recall people reporting similar problems repeatedly.
this error message usually stems from not being able to match
atom names in the .pdb file to the corresponding entries in the
.rtf file, particularly the section with internal coordinates.

it looks like your .rtf file does not seem to have any internal
coordinates so psfgen can consequently not guess them.

makes sense to me.

cheers,
   axel.

> output:
>
> reading topology
> file /home/blake/Documents/NAMD/toppar/top_all22_prot_cmap.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
> reading topology
> file /home/blake/Documents/NAMD/toppar/toppar_c35_c36/stream/toppar_all22_prot_retinol-C5-frag-redo.inp
>
> retinal/retinol and related model compounds
>
> Created by CHARMM version 32 1
> aliasing residue UNK to RTC5
> building segment C5
> disabling angle autogeneration
> disabling dihedral autogeneration
> reading residues from pdb file C5-p10-vmd.pdb
> extracted 1 residues from pdb file
> Info: generating structure...
> Info: segment complete.
> reading coordinates from pdb file C5-p10-vmd.pdb for segment C5
> Warning: failed to set coordinate for atom CT UNK:1 C5
> Warning: failed to set coordinate for atom CT2 UNK:1 C5
> Warning: failed to set coordinate for atom CT2 UNK:1 C5
> Warning: failed to set coordinate for atom CT2 UNK:1 C5
> ...............
> Info: guessing coordinates for 36 atoms (14 non-hydrogen)
> Warning: failed to guess coordinates for 36 atoms
>
> My pdb file was generated in vmd, but here are the first few lines:
> CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
> ATOM 1 CT UNK X 1 -0.621 0.576 -2.166 1.00
> 0.00
> ATOM 2 CT2 UNK X 1 -1.811 0.043 -2.987 1.00
> 0.00
> ATOM 3 CT2 UNK X 1 -3.104 0.006 -2.177 1.00
> 0.00
>
> My topology file, which was modeled after Jan Saam's for retinal:
> !read rtf card append
> * retinal/retinol and related model compounds
> *
> 32 1
>
> RESI RTC5 0.00 ! retinal C5-methyl fragment,
> ! nomenclature from PDB based on retinol
> !
> GROUP
> ATOM C1 CT 0.00
> ATOM C2 CT2 -0.18
> ATOM H21 HA 0.09
>
> My pgn file:
> package require psfgen
> topology /home/blake/Documents/NAMD/toppar/top_all22_prot_cmap.inp
> #topology /home/blake/Documents/NAMD/toppar/toppar_c35_c36/stream/toppar_all22_prot_retinol.str
> topology /home/blake/Documents/NAMD/toppar/toppar_c35_c36/stream/toppar_all22_prot_retinol-C5-frag-redo.inp
> pdbalias residue UNK RTC5
> segment C5 {
> auto none
> pdb C5-p10-vmd.pdb
> }
> coordpdb C5-p10-vmd.pdb C5
> guesscoord
> writepdb test.pdb
> writepsf test.psf
>
> And output test.pdb:
> REMARK original generated coordinate pdb file
> ATOM 1 C1 RTC5X 1 0.000 0.000 0.000 -1.00 0.00
> C5 C
> ATOM 2 C2 RTC5X 1 0.000 0.000 0.000 -1.00 0.00
> C5 C
> ATOM 3 H21 RTC5X 1 0.000 0.000 0.000 -1.00 0.00
> C5 H
> ATOM 4 H22 RTC5X 1 0.000 0.000 0.000 -1.00 0.00
> C5 H
>
> Sorry for the long email, I just haven't been able to find any good
> answers to this so far, and am getting frustrated trying to figure it
> out myself. Any help is definitely appreciated.
>
> Blake Mertz
> --
> Research Assistant
> Department of Chemistry
> University of Arizona
>
> "Life is not easy for any of us. But what of that? We must have
> perseverance and above all confidence in ourselves. We must believe
> that we are gifted for something and that this thing must be
> attained." Marie Curie
>
> "Start by doing what's necessary; then do what's possible; and
> suddenly you are doing the impossible." St. Francis of Assissi

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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