VMD-L Mailing List

From: Mgr. Lubos Vrbka (lubos.vrbka_at_uochb.cas.cz)
Date: Mon Jan 23 2006 - 08:22:43 CST

hi john & others,

> Well, as part of doing this you will have to build a psf anyway, since that's
> what psfgen does, even though it's not of any particular use when you're all
> done. It'll be helpful to force VMD to get the correct bond info etc.
> So, jut do it to please VMD and psfgen if for no other reason... :-)
> If you need help building an initial psf file for the unit cell,
> The 'autopsf' plugin should help with that.
i moved a little bit ahead. i had to firstly construct the .top file (i
modified the tip3p topology that comes with solvate plugin - i had to
add 3 atoms of type DUM) to be able to use autopsf to get the desired
psf file.

then i more or less followed the solvate plugin code. now it is clear to
me, that after i create a replica, i have to save pdb/psf file and load
it back to vmd to display it.

now there are 2 questions left

1) atoms from the original unit cell are not written to the resultant
.pdb file. i.e., if original molecules are in segment O1 (or whatever i
set it to) and the first replica atoms are in segment R1, only R1 atoms
are written to the pdb file. it doesn't cause any problems, i'll create
27 replicas instead if 26... but WHY does it behave in this way?

2) there's no problem creating the replicas, deleting the molecule and
loading it back to vmd. however, how can i do this for a trajectory? or,
how can i do the replication, do the analysis i need and the apply it to
the trajectory that is loaded in vmd?

thanks for your hints, they are really helpful!

regards,
lubos 

-- 
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Mgr. Lubos Vrbka
Center for Biomolecules and Complex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
http://www.molecular.cz/~vrbka
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