AMBER Archive (2008)

Subject: Re: AMBER: about RMSD per residue

From: Wei Huang (whuang_at_cct.lsu.edu)
Date: Wed Jul 16 2008 - 10:31:24 CDT

Hi Gustavo,

That's exactly what I want. Thanks!

Cheers,
Wei
On Wed, 2008-07-16 at 11:22 -0400, Gustavo Seabra wrote:
> Do you mean you have too many residues? If so, you can write a shell
> script to generate your ptraj.in...
>
> Something like:
>
> #!/bin/bash
>
> for file in `ls *.mdrcd`;
> do
> echo "trajin $file" >> ptraj.in
> done
>
> echo "reference foo_start.inpcrd" >> ptraj.in
> echo "image center origin" >> ptraj.in
>
> for residue in `seq -w 1 <<number of residues here>>`;
> do
> echo "rms reference mass out res_$residue.dat :1 name res_$residue
> nofit" >> ptraj.in
> done
> [...]
>
> Gustavo.
>
>
> On Wed, Jul 16, 2008 at 11:08 AM, Wei Huang <whuang_at_cct.lsu.edu> wrote:
> > Hi Ross,
> >
> > For large system, is there any convenient way to do this? Thanks!
> >
> > Best,
> > Wei
> > On Wed, 2008-07-16 at 07:52 -0700, Ross Walker wrote:
> >> trajin foo1.mdcrd.gz
> >> trajin foo2.mdcrd.gz
> >> trajin foo3.mdcrd.gz
> >> reference foo_start.inpcrd
> >> image center origin
> >> rms reference mass out res_001.dat :1 name res_001 nofit
> >> rms reference mass out res_002.dat :2 name res_002 nofit
> >> rms reference mass out res_003.dat :3 name res_003 nofit
> >> rms reference mass out res_004.dat :4 name res_004 nofit
> >> rms reference mass out res_005.dat :5 name res_005 nofit
> >> rms reference mass out res_006.dat :6 name res_006 nofit
> >> rms reference mass out res_007.dat :7 name res_007 nofit
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