VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_gmail.com)
Date: Thu Jul 08 2010 - 23:42:27 CDT

Hi Jouko,

does the topology of PCGL contain atom names like those
whose coordinates could not be set (like H22 or H23)?
I doubt it. Especially, because the next block of output
(below "Info: guessing coordinates for 30 atoms ") tells you
that many atoms are not defined in the pdb file and psfgen is
trying to guess their positions.
So, check the names of the atoms in your pdb vs. the topology file.

Btw, you may also want to check
http://terpconnect.umd.edu/~jbklauda/research/download.html
in particular
http://terpconnect.umd.edu/~jbklauda/research/download/lipid27.rtf
the file is from 2003 and seems to contain DPPC as residue

That should make it simpler.

eddi

On Thu, Jul 8, 2010 at 10:21 PM, <jouko_at_uchicago.edu> wrote:
> I am trying to make a pdb and psf for 1 DPPC molecule from
> PALM, PCGL, and the EST1 and EST2 patches, but vmd gives me
> error messages.  I am including the script which
> I used to generate the pdb, and the error messages that follow.
>
> package require psfgen
> topology top_all27_prot_lipid.rtf
> segment plm1 {pdb palm1.pdb; first none; last none}
> segment plm2 {pdb palm2.pdb; first none; last none}
> segment pcgl {pdb pcgl.pdb; first none; last none}
> coordpdb palm1.pdb plm1
> coordpdb palm2.pdb plm2
> coordpdb pcgl.pdb pcgl
> patch EST1 plm1:1 pcgl:1
> patch EST2 plm2:1 pcgl:1
> guesscoord
> regenerate angles dihedrals
> writepdb dppc.pdb
> writepsf dppc.psf
> exit
>
> Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
> Info) http://www.ks.uiuc.edu/Research/vmd/
>
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
>
> Info) Please include this reference in published work using
> VMD:
> Info)    Humphrey, W., Dalke, A. and Schulten, K., `VMD -
> Visual
> Info)    Molecular Dynamics', J. Molec. Graphics 1996, 14.1,
> 33-38.
> Info)
> -------------------------------------------------------------
> Info) Multithreading available, 8 CPUs detected.
> Info) Free system memory: 2820MB (71%)
> 1.4.5
> reading topology file top_all27_prot_lipid.rtf
>
>> CHARMM22 All-Hydrogen Topology File for Proteins and Lipids <<
>>>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<
>>>>>>>>>>>>>>>>>>>>>>>   July 2004    <<<<<<<<<<<<<<<<<<<<<<<<<<
>  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 PLM1
> reading residues from pdb file palm1.pdb
> extracted 1 residues from pdb file
> setting patch for first residue to NONE
> setting patch for last residue to NONE
> Info: generating structure...
> Info: segment complete.
> building segment PLM2
> reading residues from pdb file palm2.pdb
> extracted 1 residues from pdb file
> setting patch for first residue to NONE
> setting patch for last residue to NONE
> Info: generating structure...
> Info: segment complete.
> building segment PCGL
> reading residues from pdb file pcgl.pdb
> extracted 1 residues from pdb file
> setting patch for first residue to NONE
> setting patch for last residue to NONE
> Info: generating structure...
> Info: segment complete.
> reading coordinates from pdb file palm1.pdb for segment plm1
> reading coordinates from pdb file palm2.pdb for segment plm2
> reading coordinates from pdb file pcgl.pdb for segment pcgl
> Warning: failed to set coordinate for atom H11   PCGL:1   PCGL
> Warning: failed to set coordinate for atom H12   PCGL:1   PCGL
> Warning: failed to set coordinate for atom H21   PCGL:1   PCGL
> Warning: failed to set coordinate for atom H22   PCGL:1   PCGL
> Warning: failed to set coordinate for atom H23   PCGL:1   PCGL
> Warning: failed to set coordinate for atom H31   PCGL:1   PCGL
> Warning: failed to set coordinate for atom H32   PCGL:1   PCGL
> Warning: failed to set coordinate for atom H33   PCGL:1   PCGL
> Warning: failed to set coordinate for atom H41   PCGL:1   PCGL
> Warning: failed to set coordinate for atom H42   PCGL:1   PCGL
> Warning: failed to set coordinate for atom H43   PCGL:1   PCGL
> Warning: failed to set coordinate for atom H51   PCGL:1   PCGL
> Warning: failed to set coordinate for atom H52   PCGL:1   PCGL
> Warning: failed to set coordinate for atom O3    PCGL:1   PCGL
> Warning: failed to set coordinate for atom O4    PCGL:1   PCGL
> Warning: failed to set coordinate for atom CG1   PCGL:1   PCGL
> Warning: failed to set coordinate for atom HG11  PCGL:1   PCGL
> Warning: failed to set coordinate for atom HG12  PCGL:1   PCGL
> Warning: failed to set coordinate for atom CG2   PCGL:1   PCGL
> Warning: failed to set coordinate for atom HG21  PCGL:1   PCGL
> Warning: failed to set coordinate for atom OG2   PCGL:1   PCGL
> Warning: failed to set coordinate for atom HO2   PCGL:1   PCGL
> Warning: failed to set coordinate for atom CG3   PCGL:1   PCGL
> Warning: failed to set coordinate for atom HG31  PCGL:1   PCGL
> Warning: failed to set coordinate for atom HG32  PCGL:1   PCGL
> Warning: failed to set coordinate for atom OG3   PCGL:1   PCGL
> Warning: failed to set coordinate for atom HO3   PCGL:1   PCGL
> applying patch EST1 to 2 residues
> applying patch EST2 to 2 residues
> Info: guessing coordinates for 30 atoms (7 non-hydrogen)
> Warning: poorly guessed coordinates for 27 atoms (7 non-hydrogen):
> Warning: poorly guessed coordinate for atom H2A  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom C6   PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom C7   PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom C8   PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H5A  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H5B  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H6A  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H6B  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H6C  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H7A  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H7B  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H7C  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H8A  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H8B  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H8C  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H4A  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H4B  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom OP3  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom OP4  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom OP1  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom OP2  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H3A  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H3B  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H1A  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H1B  PCGL:1   PCGL
> Warning: poorly guessed coordinate for atom H1   PCGL:1   PCGL
> Warning: failed to guess coordinates for 4 atoms
> regenerating all angles
> regenerating all dihedrals
> Info: writing pdb file parm/dppc.pdb
> Info: Atoms with guessed coordinates will have occupancy of 0.0.
> Info: pdb file complete.
> Info: writing psf file parm/dppc.psf
> total of 136 atoms
> total of 131 bonds
> total of 257 angles
> total of 353 dihedrals
> total of 4 impropers
> total of 0 cross-terms
> Info: psf file complete.
> PLM1:1 PCGL:1
> PLM2:1 PCGL:1
> Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
> Info) Exiting normally.
> vmd >
>
>
> Thanks,
>
> Jouko
> 

-- 
--
=============================================================================
Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
=============================================================================