From: Ross Walker <>
Date: Thu 21 Nov 2002 14:30:36 -0000

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:

Zn 65.38
NE 14.01
NF 14.01

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

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

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.

  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

Loadamberparams frcmod.dat

I hope this helps

All the best

|\oss Walker

| Imperial College of Science, Technology & Medicine |
| Department of Chemistry | Theoretical Division |
| Tel:- +44 20 759(45851) |
| EMail:- |
| PGP Key available on request |

-----Original Message-----
From: sara nunez []
Sent: 21 November 2002 14:08
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
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
but once we have done so, how do we save the new.dat file which contains
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We have tried saveparmset, but leap complains is obsolete.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,

Computational Chemistry Department
University of Manchester
M13 9PL

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Received on Thu Nov 21 2002 - 06:30:36 PST
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