VMD-L Mailing List

From: Javier Goicochea (goicox_at_gmail.com)
Date: Thu Jan 15 2009 - 10:32:55 CST

Hi Christopher,

Thank you for your reply. By erasing atoms in both files the information
related to BONDS, ANGLES, DIHEDRALS, etc. gets corrupted, since the now
missing atoms are needed for these to make sense.

Perhaps, it will be easy enough to write the information for BONDS, ANGLES,
DIHEDRALS directly since I know the atoms positions in my program. Do you
know if there are guidelines to write this information?. The PSF format for
ANGLES and DIHEDRALS is quite easy to implement, I have already programmed
BONDS in my code. I am planning to use NAMD.

Regards, Javier

On Thu, Jan 15, 2009 at 5:27 PM, Christopher Gillespie <gillescche_at_gmail.com
> wrote:

> 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
>>
>
>