AMBER Archive (2002)

Subject: Re: PARMSET

From: John Bushnell (bushnell_at_chem.ucsb.edu)
Date: Thu Nov 21 2002 - 16:32:25 CST

Hi,

  I found a similar thing recently. Perhaps it is a new
thing in Amber 7, I'm not sure. After defining a couple new
atom types for treating vinyl carbons as explicitly "trans"
or "cis", I found that Amber complained about unknown atom
types. I had in a 'frcmod' file:

MASS
SC 12.01 Cis ethylene carbon
TC 12.01 Trans ethylene carbon

NONBON
  SC 1.9080 0.0860 like CM
  TC 1.9080 0.0860 like CM

etc... (higher order parameters)

  But I ended up creating a 'leaprc' type file (created by
looking at/modifying leaprc.ff99) that just looks like: (leaprc.ppv)

logFile leap.log
#
# leaprc for adding the atom types defined in ppvmod.pcy
# (This file was created by editing a copy of leaprc.ff99)
#
#
# load atom type hybridizations
#
addAtomTypes {
        { "SC" "C" "sp2" }
        { "TC" "C" "sp2" }
}
#
# Load the ppv frcmod parameters
#
parmppv = loadamberparams ppvmod.pcy
#
# Load t4r residue library
#
loadOff t4r_res.off
#

  And now, I just type "source leaprc.ppv" and it adds in
my custom atom types and parameters and sets the hybridization
and I'm ready to go. The residue library is in dat/leap/lib,
the parameter file is in dat/leap/parm, and the leaprc file is
in dat/leap/cmd.

  I'm not sure this is your problem, but it confused me for a bit...

      HTH - John

On Thu, 21 Nov 2002, sara nunez wrote:

> Dear amber users,
>
> We are trying to load a parameter file in leap which contains all the
> special parameters for our non-standard atoms.
> The problem is that leap recognises the bonds, dihedrals, etc. in out .dat
> file, but not the atoms types! (and the atom types ARE in the .dat file)
> We were wondering where we may have gone wrong.
>
> Our alternative was to edit by hand the atom types in the PARMSET editor,
> but once we have done so, how do we save the new.dat file which contains our
> the input atom types?
> We have tried saveparmset, but leap complains is obsolete. Is there any
> alternative to save our new .dat file with the added parameters?
>
> All suggestions are much appreciated.
>
> Thank you very much,
> sara
>
> Computational Chemistry Department
> University of Manchester
> Manchester
> M13 9PL
>
>
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