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.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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Received on Sun Jul 20 2008 - 06:07:11 PDT
