VMD-L Mailing List

From: denilson_at_dqi.ufla.br
Date: Thu Oct 06 2011 - 15:12:44 CDT

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.