AMBER Archive (2009)

Subject: Re: [AMBER] rms fit of mutant with respect to wild type structure

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Oct 29 2009 - 09:03:35 CDT

ptraj assumes you are comparing the same molecules. if not, the atoms won't
match.

On Thu, Oct 29, 2009 at 9:55 AM, Siddharth Rastogi <
siddharthrastogi08_at_gmail.com> wrote:

> Dear Amber users,
> I am interested to get RMS fit of Mutant with respect to wild type
> structure. I have used the following input file
>
> reference 1WT.pdb
> trajin MUT_prod_1_1ns.mdcrd.gz 1 1 1
> strip :WAT
> strip :Cl-
> center :1-100_at_CA
> image center familiar
> rms reference out rmsd_WT_MUT :1-100_at_CA
>
> The value obtained from the output file is around 4 Angstroms. But I got
> 0.8 Angstroms using Chimera for the same two structures. There is some
> problem with the above syntax it seems. But I am not getting the problem.
> Can anyone help me in this regard.
> --
> Siddharth Rastogi
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>
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