AMBER Archive (2004)

Subject: RE: AMBER: sander.QMMM: CHARGE keyword in file

From: Ross Walker (
Date: Wed Aug 04 2004 - 15:48:08 CDT

Dear Bud,

> A question about sander.QMMM (AMBER8) input.

First question, have you applied bugfix.13? If not, do this first of all
before you do ANY QMMM calcs.
The charge you specify in should be just the charge on the QM
system. Bare in mind however that any bond you break will have hydrogen
atoms added in the QM region. E.g:

 H H H H QM region = C1 and C2 H H
HC1-C2-C3-C4H ------------------------> HC1-C2H Charge =0
 H H H H H H

Hence check if you are breaking bonds and where. Then for every bond you
break add a hydrogen on the QM section and at the end of it see what you are
left with. Then calculate charge of this QM piece and set that in the file.

If you still have problems please email me your input files and I'll take a
look and see if I can get it to run.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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