AMBER Archive (2008)

Subject: RE: AMBER: QM/MM: input conversion error

From: Ross Walker (
Date: Thu Jan 24 2008 - 18:01:43 CST

Hi Pankaj,

> > iqmatoms= '@3038-3043, 3050-3055, 7028-7039, 7053-7105',
> Well, I never quote (') or use @ in my iqmatoms list. Maybe leave
> them out? I think iqmatoms is just a comma-separated list of QM
> atoms. That is the way I specify it in my simulations, and they seem
> to work just fine. Ross or Gustavo can correct me if I am wrong.

Bud is correct here. There are two mutually exclusive ways of specifying the
QM atoms in AMBER 9. You can either use iqmatoms which should just be a
comma seperated list of integers or you you can use qmmask='' in which case
you can include a definition in AMBER mask format inside the quotes.

So in your case you either want to use:

qmmask = '@3038-3043, 3050-3055, 7028-7039, 7053-7105',

although off the top of my head I can't remember if you need the @ symbol
before each range or not.

or you would need:


Good luck,


|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to