AMBER Archive (2008)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
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:

iqmatoms=3038,3039,3040,3041,......

Good luck,

Ross

/\
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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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