AMBER Archive (2002)

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

From: William Wei (william_at_phm.utoronto.ca)
Date: Wed Aug 14 2002 - 16:52:34 CDT

Hi, Good afternoon, my purpose is get the snapshots from my dynamics
simulation using carnal. Can carnal do that? I tried to get it, but I
failed. Here is my input file for carnal. Can anybody help me to figure it
out? Thanks.

William.
-------------------
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

-------------------------
William Wei
Faculty of Pharmacy
19 Russell Street
Toronto, ON. M5S 2S2
Tel: 1-416-946-8469
Fax: 1-416-978-8511
Email: william_at_phm.utoronto.ca
       william.wei_at_utoronto.ca