On Fri, Jun 27, 2014 at 5:46 PM, Chinthaka Ratnaweera <cnr88.msstate.edu>
wrote:
> This is not I meant.
> Lets say, I have two pdb structures of the same protein, which generated
> through average md trajectories after different interactions. These two
> structures are slightly different. I want to find out the rmsd between
> them. I know VMD can do that. But I want to know whether it is possible in
> ptraj or cpptraj?
>
Yes. cpptraj can do it. If you type "help rmsd" in the cpptraj command
prompt, you will see a "perres" keyword that should do what you want it to
do.
*$* cpptraj
CPPTRAJ: Trajectory Analysis. V15.01b
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
> help rmsd
[<name>] <mask> [<refmask>] [out filename] [nofit | norotate] [mass]
[ first | reference | ref <name> | refindex <#> |
reftraj <filename> [parm <parmname> | parmindex <#>] ]
[perres perresout <filename> [perresavg <avgfile>]
[range <resRange>] [refrange <refRange>]
[perresmask <additional mask>] [perrescenter] [perresinvert]
Calculate coordinate root-mean-squared deviation of atoms in <mask>
>
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jun 27 2014 - 16:00:02 PDT
