Re: [AMBER] How to put the restrain on just part of the system.

From: David A Case <>
Date: Sun, 27 Aug 2017 16:45:10 -0400

On Sun, Aug 27, 2017, Parviz Seifpanahi Shabane wrote:

> I need to put a restraint on just part of my proteins during the production
> step. My system is the slice of Nucleosome ( the mixture of DNA and histone
> protein), first I created the PDB file from my topology and coordinate
> files by "ambpdb", from this PDB files I found the residue number which I
> wanted to be free (residue 111 to 134). I tried different methods for
> applying restraint (below), but none of them worked. I checked "mdout" file
> the restrained energy in all of the cases is zero.

Did you set ntr=1 in the cntrl namelist?

The restrainmask syntax is much simpler, e.g.

   ntr=1, restraint_wt=10.0, restraintmask=":1-110,135-201",

will restrain all residues in the range 1-201 except for 111-134. You don't
need any group cards here.

...hope this helps....dac

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Received on Sun Aug 27 2017 - 14:00:03 PDT
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