VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Aug 14 2007 - 10:56:07 CDT

Hi Thomas,
the easiest solution is probably to go back to however you deleted
atoms, and delete whole residues instead (eg, "same residue as (SELECTION)")

In general, you can use psfgen with the appropriate topology file
downloaded from
http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm, but
this will not solve your problem because the partial residues will still
be completed...

Peter

Θωμας Ευαγγελιδης wrote:
> Peter,
> I need that psf mainly for visualization ,but it would be better if I could use
> it for both visualization and simulation. The atoms I deleted were only water
> molecules and ions. But some water molecules were not deleted as a whole (I
> just deleted the OH, the H or the O from them). So I suspect that those lines I
> mentioned in my previous message (which were red or white, were starting from a
> common point and were ending at an incomplete water molecule) are bonds between
> atom/s deleted and the other part of the water molecule left. Is it feasible to
> find which atoms are absent from those incomplete molecules, in order to avoid
> deleting them and see if that will work?
> As for the psfgen plugin I think that it needs a topology file. Which one should
> I use?
> Thanks for your help,
> Thomas
>
>
>
> Αρχικό μήνυμα από Peter Freddolino <petefred_at_ks.uiuc.edu>:
>
>
>> Hi Thomas,
>> this is certainly possible to do; there are a couple of different
>> possibilities. Do you need this psf you want to create for visualization
>> or simulation? If you only need to visualize things, you can just use
>> the $sel writepsf command; this will write atoms and bonds, but not
>> angles or dihedrals (so it isn't appropriate for simulation).
>>
>> If you need a "real" psf you'll probably need to use psfgen manually. If
>> you're deleting some sections of protein or certain atoms from complete
>> residues, autopsf is probably adding in termini where you've made gaps.
>> It would help if you could be more specific about what you've deleted.
>> If your modified pdbs have *incomplete* residues, then psfgen will
>> complete them based on standard topologies.
>>
>> Also, for writing dcds, you should try the "animate write" command...
>>
>> Peter
>>
>>
>>
>
>
>