Re: AMBER: md output file

From: Gustavo Seabra <>
Date: Thu, 03 May 2007 07:32:56 -0400

deepti nayar wrote:
> hi all
> i ran a simple molecular dynamics on amber9 with the following script
> . i have tried to restrain few atoms here. but when i look at the
> output file, it seems to me that the belly command has not worked out.
> i am attaching my output file also. please anyone let me know how to
> restrain atoms.
> with regards
> deepti
Notice that the syntax you used is definitely *not* the recommended
Amber9 syntax, which uses 'ibelly' and a 'bellymask'. still, this will
not accomplish what you want, since the "belly" defines the *moving*
atoms in the system, not the frozen ones. To restrain specific atoms,
you should use 'ntr=1' instead, and provide a restraint_wt and a

Please look at the section "5.6.4. Frozen or restrained atoms." in the
Amber9 manual for details.

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Received on Sun May 06 2007 - 06:07:17 PDT
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