AMBER Archive (2002)

Subject: Re: Can we get trajectories coordinates after FIT in Carnal?

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Wed Aug 14 2002 - 16:29:41 CDT

Hi William,

modify the line

COORD c1 s1 MOD 10 ATOM 8328;
to
COORD c1 rms1 MOD 10 ATOM 8328;

in your script below.

This means, you will take coordinates to dump from the stream "rms1"
instead of the original coordinate stream "s1".

Best regards

Holger

> FILES_IN
> # Input the parm.top file, and the coordinates.
> PARM p1 CMVDimer.top;
> STREAM s1 CnsP_51.2_90.6psR_mdcrd.Z
> CnsP2.5_3nsR_mdcrd.Z;
> STATIC ref1 CMVDimer.crd;
>
> FILES_OUT
> COORD c1 DimerTrj.pdb PDB;
>
> DECLARE
> GROUP g1 (((RES 209-222, 457-470))&(ATOM TYPE CA));
>
> RMS rms1 FIT g1 s1 ref1;
>
> OUTPUT
> COORD c1 s1 MOD 10 ATOM 8328;
>
> END 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++