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
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Wu Lei
> Sent: 14 July 2004 21:13
> To: amber.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.scripps.edu>
> To: <amber.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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> >
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Received on Thu Jul 15 2004 - 05:53:00 PDT
