Thanks a lot!
i've tried both method,and it works! but new problem arised, when using "saveamberparm" command, new error message has appeared:
For atom .... Could not find type: CK
....
but there is { "CK" "C" "sp2" } in addatomtypes section in leaprc file.
is any where else should i add the atomtype definition in leap input files?
Thanks!
----- Original Message -----
From: "Ross Walker" <ross.rosswalker.co.uk>
To: <amber.scripps.edu>
Sent: Thursday, July 15, 2004 12:20 PM
Subject: RE: AMBER: How to apply OPLS force field?
> 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
> > >
> > >
> > --------------------------------------------------------------
> > ---------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber.scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> > >
> > --------------------------------------------------------------
> > ---------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Jul 15 2004 - 08:53:00 PDT
