From: Venky (venky.agas_at_gmail.com)
Date: Sat Jul 28 2007 - 03:45:05 CDT
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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