AMBER Archive (2002)

Subject: RE: PARMSET

From: Ross Walker (r.c.walker_at_ic.ac.uk)
Date: Thu Nov 21 2002 - 08:30:36 CST

Dear Sara,

Are you also specifying the masses for your new atom types along with
their non bonding parameters. E.g a modified parameter file that I use
is as follows:

MASS
Zn 65.38
NE 14.01
NF 14.01

BOND
Zn-NB 85.5 2.101
Zn-O 45.1 2.359
NF-CG 420.0 1.355

ANGL
Zn-O-C 19.9 131.2
NB-Zn-O 16.1 97.9
NE-CE-CF 85.0 113.0

DIHE
H1-CT-OH-Zn 1 0.06 0.00 3.
CA-CT-OH-Zn 1 0.06 0.00 3.
H1-CT-Zn-SH 1 0.18 0.00 3.

NONB
  Zn 1.85 0.06
  NE 1.8240 0.170
  NF 1.8240 0.170

I simply load this into xleap before loading any pdbs etc using the
command

Loadamberparams frcmod.dat

I hope this helps

All the best
Ross

/\
\/
|\oss Walker

| Imperial College of Science, Technology & Medicine |
| Department of Chemistry | Theoretical Division |
| Tel:- +44 20 759(45851) |
| EMail:- ross_at_rosswalker.co.uk | http://www.rosswalker.co.uk/ |
| PGP Key available on request |

-----Original Message-----
From: sara nunez [mailto:mbdtssn_at_hotmail.com]
Sent: 21 November 2002 14:08
To: amber_at_heimdal.compchem.ucsf.edu
Subject: PARMSET

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We have tried saveparmset, but leap complains is obsolete.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

_________________________________________________________________
MSN Fotos: la forma más fácil de compartir e imprimir fotos.
http://photos.msn.es/support/worldwide.aspx