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.rosswalker.co.uk |
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Received on Sun Jan 27 2008 - 06:07:23 PST
