Re: [AMBER] Distance Restraint using COM for Umbrella Sampling

From: Daniel Roe <>
Date: Tue, 29 Aug 2017 15:29:06 -0400


The 'rst' command in cpptraj can convert regular Amber mask
expressions to Amber group format. For example:

> rst :1 :12 r1 2 r2 3.5 r3 3.5 r4 5 rk2 5 rk3 5
    Mask [:1] corresponds to 13 atoms.
    Mask [:12] corresponds to 22 atoms.
 &rst iat=-1,-1,0
   r1=2.000000, r2=3.500000, r3=3.500000, r4=5.000000, rk2=5.000000,
   nstep1=0, nstep2=0,

See the manual for full details.


On Tue, Aug 29, 2017 at 8:56 AM, Suchetana Gupta <> wrote:
> Dear Amber users
> I want to perform umbrella sampling on my protein of interest. What will be
> the format for specifying the COM of certain residues (say I want to apply
> restraint on residues x to y)? I realised that I can manually write all the
> atom numbers using iat and igr, but is there any existing format to do it
> automatically? Also, is it true that the iat can read only upto 200 atoms
> at a time?
> Thanks in advance
> Suchetana Gupta
> IIT Madras
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Tue Aug 29 2017 - 12:30:03 PDT
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