VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Oct 13 2011 - 10:33:26 CDT

Hi,
  The PDB format doesn't include complete bond information, so any
CG structures you create as a PDB file won't display quite right without
a matching PSF file. The AutoPSF plugin can't cope with CG structures, so
that's the reason you ran into trouble there. You will have to generate
the PSF file either using the CG builder tools or with your own scripts
via psfgen.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Oct 06, 2011 at 05:12:44PM -0300, denilson_at_dqi.ufla.br wrote:
> Dear all,
>
> In order to carry out a coarse grained simulation I am using VMD 1.9 (32
> bits) on a Windows 7 (64 bits) to prepare the input files for NAMD 2.8
> (Charmm force field). At first, I converted a pdb file containing the
> structure of a protein and some molecules of water to the corresponding
> psf and pdb files by the use of Autopsf with the topology file inside VMD.
> Then, I used Solvate (solvate file.psf file.pdb -t size -o outputfile) to
> put my protein inside a water box. In the next step I used the CGBuilder
> with default parameters to obtain the residue-based coarse grained pdb and
> rcg files. The result seemed strange to me, since when viewed as line or
> cpk representation there was no bond (link) between the beads of the
> protein structure in the pdb file. Is it normal ? Anyway, I moved on to
> the next step that comprised transformation of the coarse grained pdb file
> into de corresponding pdb and psf file by the use of Autopsf with the
> topology file rbcg-2007.top. I did not succeed in this step, since an
> error ocurred when Autopsf was running. Here is the log file of Autopsf:
>
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> while executing
> "segment $segid {
> pdb $segfile
>
> # We alias the C-terminal OXT atoms to OT2 so that psfgen has to
> guess one atom less.
> # Otherwise psf..."
> (procedure "psfsegments" line 37)
> invoked from within
> "psfsegments $logfileout"
> (procedure "psfmain" line 63)
> invoked from within
> "psfmain"
> (procedure "::autopsf::runpsfgen" line 35)
> invoked from within
> "::autopsf::runpsfgen"
> invoked from within
> ".autopsf.gobutton invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 24)
> invoked from within
> "tk::ButtonUp .autopsf.gobutton"
> (command bound to event)
>
> I would appreciate if somebody could help me to solve this problem.
>
> Best regards.
>
> Denilson.
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078