RE: guesscoord fails, hydrogen adding problem, output pdb is all zeros

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Jul 28 2007 - 10:06:45 CDT

You're missing a step. Psfgen doesn't know anything about molecules you've
loaded in VMD. It has to be told explicitly where to look for coordinate
information.

 

3.5. coordpdb xrr.pdb XR

 

With that, everything should work.

 

  _____

From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Venky
Sent: Saturday, July 28, 2007 3:45 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: guesscoord fails, hydrogen adding problem, output pdb is
all zeros

 

Hi NAMD users,

My system is a membrane protein with one of the residues subsititued for a
unnatural residue. The params and topology for this unnatural residue has
been parameterized and I included it in the charmm topology file as an added
residue. And provided this file for preparing the files in VMD. I have a
lot of hydrogens missing from the pdb file. Here is what I do step by step

1. mol load pdb xrr.pdb
(returns the mol id)

2. pdbalias residue HIS HSE
(returns aliasing residue HIS to HSE)

3. segment XR {
pdb xrr.pdb
}

returns
building segment XR
reading residues from pdb file xrr.pdb
extracted 241 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.
Info: skipping bond C-N at end of segment.
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping cross-term C-N-CA-C-N-CA-C-N at end of segment.
Info: skipping conformation CA-C-N-CA at end of segment.
Info: skipping conformation N-CA-C-O at end of segment.
Info: skipping conformation N-CA-C-N at end of segment.
Info: segment complete.

4. guesscoord (here is where it fails)
returns
Info: guessing coordinates for 3857 atoms (1906 non-hydrogen)
Warning: failed to guess coordinates for 3857 atoms

5. writepsf xrr.psf
Info: writing psf file xrr.psf
total of 3857 atoms
total of 3911 bonds
total of 7070 angles
total of 10345 dihedrals
total of 583 impropers
total of 238 cross-terms
Info: psf file complete.

the psf file generated looks good and all the information about missing
hydrogens are included in the psf generated.
but when I write the pdb file out the coordinates of all the atoms are 0 0
0!
not sure where the problem here lies...

Thanks in advance

Venky

~ You will become rich and famous, unless you don't.

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