AMBER Archive (2004)

Subject: Re: AMBER: How to apply OPLS force field?

From: Wu Lei (wulei_at_biophy.nju.edu.cn)
Date: Wed Jul 14 2004 - 23:12:50 CDT

Thanks a lot! :-)

i think i've found the cause of the problem.

it's originated from the confliction of atom type in residue library and the opls force field.
the leaprc file loaded both all_amino94.lib all_aminoct94.lib and all_aminont94.lib. these residue templates defined atom types which are much different from atom types used in opls_parm.dat. so when pdb files loaded, the residue template have defined the atom types which could not be recognized by opls force field.
maybe i have to modify the amino acid library files to use the "united atom types".

wl

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Thursday, July 15, 2004 12:29 AM
Subject: Re: AMBER: How to apply OPLS force field?

> On Wed, Jul 14, 2004, Wu Lei wrote:
>
> > i have problem on applying OPLS force field.
> > The atom type defined in opls_parm.dat is much different from the atom
> > types in pdb, so it causes problems when creating input files in leap.
>
> You will have to specify your problem more precisely. PDB files don't have
> any information about atom types, so there cannot be any direct conflict
> between a PDB file and a force field. You will have to say what you tried,
> and what the result was.
>
> Note also: the OPLS files in Amber refer to a very old version of that force
> field (I think from 1988). So you should make sure that this is what you
> really want.
>
> ...good luck...dac
>
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