Hi,
If you just want the distance between residues 307 and 381 why not use:
distance d307-381 :307 :381 out d307-381.dat
-Dan
On Friday, May 10, 2013, Chris Chris wrote:
> I'm trying to use drmsd in cpptraj to follow the distance between residues
> 307 and 381.
>
> I used the following .in file
>
> trajin 2psj_2ctz_112812_prod.mdcrd
> trajin 2psj_2ctz_112812_prod1.mdcrd
> trajin 2psj_2ctz_112812_prod2.mdcrd
> reference 2psj_2ctz_112812_equil1.rst
> drmsd reference out 2psj_2ctz_prod5ns.dat :307 :281
>
> Is there a mistake here? It won't run, I got the following in the .out
> file:
>
> PARAMETER FILES:
> 0: 2psj_2ctz_112812.prmtop, 39813 atoms, 11904 res, ortho. box, 11599
> mol, 11591 solvent mol, 2519 frames
>
> REFERENCE COORDS:
> [2psj_2ctz_112812_equil1.rst] is an AMBER restart file with velocity
> info, Parm 0 (with box info) (reading 1 of 1)
> The following 1 frames have been defined:
> 0: 2psj_2ctz_112812_equil1.rst frame 1
> Active reference frame for masks is 0
>
> OUTPUT TRAJECTORIES:
> No files.
>
> Thanks for any help
> Chris
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Sat May 11 2013 - 08:30:02 PDT
