AMBER Archive (2008)

Subject: Re: AMBER: about RMSD per residue

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Wed Jul 16 2008 - 10:22:39 CDT

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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu