Re: Building PSF file for protein with ions

From: ehenriques_at_qui.uc.pt
Date: Wed Sep 01 2010 - 09:02:17 CDT

looks like a problem with the naming of the atoms in your amino2.pdb file.
The naming of the non-hydrogens atoms in proteins are usually standard
and PDB names match with the force-field's. For the hydrogens and
C-terminal oxygen(s) each force-field has it's own naming scheme,
hence some of the names are not recognized by psfgen (that's the
'failed to set coordinate for atom' warning).
Since you used the command 'guesscoord', psfgen tries to assign
coordinates to the missing atoms (and sometimes you get the 'poorly
guessed coordinate for atom' warning).
As an example, atom O of SER:381 of your pdb file should be named OT1
if you want to preserve its coordinates.

Hope it helps,

Elsa

Quoting "anas ." <orbit1984_at_hotmail.com>:

>
>
> 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
>
>
>

-- 
Elsa S. Henriques                     e-mail: ehenriques_at_qui.uc.pt
Investigadora Auxiliar
Biologia Estrutural e Computacional (@CNC)
e Grupo de Química Estrutural (@CCC)
Cv15 - RMB Lab
Departamento de Química - Universidade de Coimbra
3004-535 COIMBRA                         Portugal
Tel.: +351 23 9852080 - ext.417
Fax : +351 23 9827703

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:28 CST