Re: Calcium ions and psfgen

From: V.Ovchinnikov (ovchinnv_at_MIT.EDU)
Date: Wed Sep 17 2008 - 18:12:18 CDT

Looks to me like you might need a
'pdbalias atom CA CAL'
in there


PS. The VMD forum is a better place to post this

On Wed, 2008-09-17 at 17:53 -0400, MIke S wrote:
> Hi,
> Could someone help me out?
> I'm working with a calcium binding protein and I'm trying to create
> the PSF and PDB files using psfgen, but I'm running into some problems
> in generating the coordinates for the calcium ions.
> I created 2 segments, one for the protein and one for the 4 calcium
> ions, by using modified PDB files as required. I made sure that the
> atom and residue names for the calcium ions match the topology file by
> using the pdbalias commands, and I included the 'first none' 'last
> none' patch commands in building the caclium segement (as suggested in
> the topology file).
> The relevant portion of the script is:
> topology (directory and filename of topology file)
> pdbalias residue CA CAL
> pdbalias CAL CA CAL
> segment cal {
> first none
> last none
> pdb (directory)/calcium.pdb
> }
> coordpdb (directory)/calcium.pdb cal
> For some reason I keep getting the following error message:
> setting patch for first residue to NONE
> setting patch for last residue to NONE
> reading residues from pdb file /calcium.pdb
> extracted 4 residues from pdb file
> Info: generating structure...
> Info: segment complete.
> % % .pdb cal
> Warning: failed to set coordinate for atom CA CA:148 CAL
> Warning: failed to set coordinate for atom CA CA:149 CAL
> Warning: failed to set coordinate for atom CA CA:150 CAL
> Warning: failed to set coordinate for atom CA CA:151 CAL
> The resulting pdb file has all the right coordinates for the protein
> but the coordinates for the calcium ions are set to zero.
> To circumvent the problem I considered just cutting and pasting the
> original calcium coordinates into the psfgen-generated pdb file, but
> that would obviously lead to errors in my psf file. So, I'm kind of
> stuck as to what I should do. Your suggestions are appreciated.
> Cheers,
> Mike

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:50 CST