Use VMD to visualise your molecule - this is an excellent program for
animating trajectories and analysing structural changes over the course of
an MD run. It loads prmtop and restart files as well as pdbs, and is
available from the website
http://www.ks.uiuc.edu/Research/vmd/.
Alternatively, resize the MAXATM parameter in the source code for pdbgen, or
try using ambpdb or carnal to generate your pdbs.
Good luck,
Halima
--------------------------------------------------
Halima Amer
Department of Chemistry
Imperial College of Science, Technology & Medicine
Exhibition Road
South Kensington
London SW7 2AY
Tel: 020-7594-5851
Fax: 020-7594-5806
http://defiant.ch.ic.ac.uk/~halima
--------------------------------------------------
-----Original Message-----
From: Michael Cooney [mailto:mike_at_bmbiris.bmb.uga.edu]
Sent: 20 September 2000 16:55
To: amber_at_cgl.ucsf.edu
Subject: Loading CRD or RST files into Leap
To all Amber users,
I have just recently started using Leap with Amber6 and would like
to know if there is a way to load a coordinate (or restart) file
directly into XLEaP, e.g. to visualize a molecule where minimization
or MD has just been carried out, and to proceed further on that structure.
Some solvated molecules are too big for pdbgen to handle (max. 12000
atoms).
I would appreciate any suggestions--I looked in the manual but didn't
find any such command.
Thank you very much,
Sincerely,
Michael G. Cooney
Department of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602, USA
Received on Wed Sep 20 2000 - 09:57:47 PDT
