Re: Calcium ions and psfgen

From: MIke S (vmd.namd_at_gmail.com)
Date: Wed Sep 17 2008 - 18:18:47 CDT

Victor,

Thanks for the quick reply and for reminding me that I need a new pair of
glasses. What a silly mistake!

Take care,

Mike

On Wed, Sep 17, 2008 at 7:12 PM, V.Ovchinnikov <ovchinnv_at_mit.edu> wrote:

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

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