AMBER Archive (2004)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jul 14 2004 - 23:20:58 CDT


That's one option.

Alternatively you could try loading the opls_nacl.in, opls_unict.in,
opls_uni.in and opls_unint.in files in $AMBERHOME/dat/leap/prep.

Although I personally have never tried using the OPLS force field with leap
so this may or may not help.

All the best
Ross

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|\oss Walker

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Wu Lei
> Sent: 14 July 2004 21:13
> To: amber_at_scripps.edu
> Subject: Re: AMBER: How to apply OPLS force field?
>
> 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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