AMBER Archive (2002)

Subject: Re: carnal output trajectory

From: Sanjeev B.S. (sanjeev_at_mbu.iisc.ernet.in)
Date: Wed Oct 30 2002 - 07:50:45 CST

I could not do a single step carnal, so settled with two step. Later I
used ptraj to do the task. The example in ptraj does not work, 'cos the
sequence of the commands are upside down! the following is the one that I
presently use to do the job to generate PDBs fitted with a reference
structure and the molecule placed at center of the box. Hope this helps. 

---

reference  /home/sanjeev/MD/1HI2/INPUT-MINIM/molecule.min.crd

trajin     /home/sanjeev/MD/1HI2/CRD/molecule.0000_0010.crd.gz
trajin     /home/sanjeev/MD/1HI2/CRD/molecule.6370_6380.crd.gz
trajin     /home/sanjeev/MD/1HI2/CRD/molecule.6380_6390.crd.gz
trajin     /home/sanjeev/MD/1HI2/CRD/molecule.6390_6400.crd.gz

trajout molecule.pdb PDB

center @CA
image

rms reference out CAmolecule.rms @CA

go

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On Wed, 30 Oct 2002, Vlad Cojocaru wrote:

Dear Amber users,
  I found out that OUTPUT COORD option in carnal has an option BOX which 
is not written in the manual.
  With this option I managed to output trajectories in a proper way for 
visualizing them with VMD.
  Now the question is that I want to see the trajectory after fitting 
all the structures to the first frame.
  The BOX option seems not to work anymore when I give to carnal the 
following:
DECLARE
   GROUP g1 (RES 1-17);   
   IMAGE img g1%cmass;
   RMS fit1 FIT g1;
OUTPUT
   COORD crd fit1 BOX;
The program gives an error message that tells me that the BOX option 
does not work with fit. If I do not use the BOX option the trajectories 
are again impossible to visualize with VMD.
 Does anyone have any suggestions about this??
Thanks a lot!
vlad