VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Sep 21 2007 - 07:27:34 CDT

>
> But I think that if you want to use your .psf for simulations, you must not
> modify the topology file.
>
>
Just to clarify, I can't speak to charmm, but at least in namd there's
no need for that H1-H2 dummy bond; it is fine to use a psf based on a
modified topology file. It used to be needed for rigidbonds, but now has
no effect in namd (you'll note that this bond has a constant of 0 in the
parameter file).
Peter
> Good luck,
> Thomas Evangelidis
>
>
>
>
>> Dear all,
>> I am trying to generate a PSF file from a PDB which contains water
>> molecules. I used AutoPSF VMD plugin but it did not work. I tried
>> using "pdbalias residue HOH TIP3" in a file but it did not work as well.
>> Do you have any suggestions?
>>
>> Andrea Cristiani
>>
>> LCT-Biochimie Pharmaceutique
>> Universitι de Genθve
>>
>>
>>
>>
>
>
>