AMBER Archive (2004)

Subject: Re: AMBER: Sander & fix atoms

From: Viktor Hornak (
Date: Thu Jun 03 2004 - 12:22:55 CDT wrote:

>Hello, Amber:
>I would like to run energy minimization in sander with some restrictions.
I'd suggest to use positional restraints (rather than fixing atoms =
ibelly flag) - check ntr flag in amber manual. You don't say which
version of amber you are using. Depending on that your input file might
look differently.
In amber8, you'd specify 'restraint_wt' and 'restraintmask' in your
&cntrl input section. This could translate to the following for what you
want (if I understood your description of restrictions well):

>How can I set the minimization inputs with following restrictions:
>--- fix heavy (all but hydrogens) atoms

>--- fix backbone atoms

>--- fix backbone atoms with tethered heavy atoms
restraintmask='@CA,C,O,N' (?? - maybe that's not what you want but you
get an idea)

>--- tethered backbone atoms
restraintmask='@O,H' (??)

Check chapter 11.5 in amber8 manual for more detailed description of
selection syntax.

If you are using amber7 or previous, carefully read "GROUP
specification" appendix in amber manual.

Hope this helps...


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