Building PSF file for protein with ions

From: anas . (orbit1984_at_hotmail.com)
Date: Wed Sep 01 2010 - 05:22:50 CDT

Hi Guys,

I am using NAMD version 2.7b1 in Windows XP Professional (64x edition), I am
trying to build a PSF file for a protein with few Ca ions but the resultant PSF file
contains amino acids only and no calcium ions, it also failed to set coordinates
for atoms. I checked other related posts and tried creating 2 separate PDB files,
one for amino acids and the other for calcium ions only but had the same
problem. This is my PGN file:

package require psfgen
topology top_all27_prot_lipid.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
pdbalias CA CAL
segment U {pdb amino2.pdb}
coordpdb amino2.pdb U
segment cal {pdb Ca2.pdb}
coordpdb Ca2.pdb cal
guesscoord
writepdb templaten.pdb
writepsf templaten.psf

I also used the following commands to create the 2 PDB files:

set amino [atomselect top protein]
$amino writepdb amino2.pdb

AND

set Ca [atomselect top protein]

$Ca writepdb Ca2.pdb

This is the end part of the PSF file output:

Warning: failed to set coordinate for atom H THR:378 U
Warning: failed to set coordinate for atom H ASP:379 U
Warning: failed to set coordinate for atom H ARG:380 U
Warning: failed to set coordinate for atom O SER:381 U
Warning: failed to set coordinate for atom H SER:381 U
Warning: failed to set coordinate for atom H SER:381 U
Warning: failed to set coordinate for atom HG SER:381 U
building segment CAL
reading residues from pdb file Ca2.pdb
extracted 0 residues from pdb file
Info: generating structure...
Info: segment complete.
reading coordinates from pdb file Ca2.pdb for segment cal
Info: guessing coordinates for 430 atoms (2 non-hydrogen)
Warning: poorly guessed coordinates for 5 atoms (2 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1 LYS:29 U
Warning: poorly guessed coordinate for atom HT2 LYS:29 U
Warning: poorly guessed coordinate for atom HT3 LYS:29 U
Warning: poorly guessed coordinate for atom OT1 SER:381 U
Warning: poorly guessed coordinate for atom OT2 SER:381 U
Info: writing pdb file templaten.pdb
Info: Atoms with guessed coordinates will have occupancy of 0.0.
Info: pdb file complete.
Info: writing psf file templaten.psf
total of 5336 atoms
total of 5396 bonds
total of 9720 angles
total of 14256 dihedrals
total of 954 impropers
total of 351 cross-terms
Info: psf file complete.

Could anyone give me any insights to what I am missing here?

Any help is really appreciated, thanx!

Best Regards,
Anas Sultan

                                               

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