VMD-L Mailing List

From: Christopher Gillespie (gillescche_at_gmail.com)
Date: Thu Jan 15 2009 - 10:27:52 CST

Javier,

I will have to think about this one. Since you did not tell it to
generate new atoms I not sure why you have new ones. I guess a quick
and dirty fix is to delete all the atoms in the psf and pdb files that
were added with positions 0,0,0. But this change is not much
different than your original idea.

Maybe someone else who is more familiar with the internals of the
psfgen and writepsf can make some more suggestions.

Best

Chris

On Jan 15, 2009, at 11:11 AM, Javier Goicochea wrote:

> Hi Christopher,
>
> Thank you for your prompt reply. I tried your script and worked. The
> only modification I did, was to change "Quartz" by the name of my
> PDB file (MB_PDB01.pdb). Unfortunately, the new PDB and PSF files
> have more atoms than my original PDB file. The new number of atoms
> is a multiple of 9. All new atoms are created at 0,0,0, so I guess
> writepsf also follows the information in the TOP file.
>
> In my case, I was using the following script to create the PSF file
> (without calling guesscoord):
>
> psfcontext reset
> topology MB_PDB01.pdb.inp
> segment X147 {pdb MB_PDB01.pdb}
> writepsf MB_PDB01.pdb.psf
>
> X147 is just a dummy name.
>
> Regards, Javier