AMBER Archive (2009)

Subject: RE: [AMBER] Regarding syntax for freezing different atoms

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Apr 23 2009 - 08:24:55 CDT

Hi Jorgen

> 1. Is it possible with a simple command to freeze all non-hydrogen
> atoms?
>
> 2. If I want to freeze atom 1-9 and then 20-60 how do I do that for 1-9
> I
> would do the following
> &cntrl
> imin=1,
> maxcyc=10000,
> ncyc=5000,
> ntb=0,
> ntc=1,
> cut=12,
> ntr=1
> /
> Hold the atoms fixed
> 500.0
> RES 1 9
> END
> END

You can use the amber mask approach for this (although it only works in
sander) you need to use the group specification for pmemd.

Here's an example:

&cntrl
  imin=1,
  maxcyc=10000,
  ncyc=5000,
  ntb=0,
  ntc=1,
  cut=12,
  ntr=1
  imin=1, maxcyc=200, ntb=0, cut=99,
  ntpr=5, ntr=1,
  restraint_wt=500.0, restraintmask='@1-9,20-60'
 /

If you wanted to restrain all non hydrogen atoms then you would write
something like:

restraintmask='!@H='

The mask specification is discussed in Section 11.3 of the AMBER 10 manual.

Additionally the specs for GROUP input (the old style you have in your
example) are provided in appendix B of the AMBER 10 manual.

All the best
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 |
| http://www.rosswalker.co.uk | PGP Key available on request |

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