Re: Questions about output archive and micromolecules

From: David A. Case <>
Date: Tue, 1 Jul 2003 10:39:33 -0700

On Mon, Jun 30, 2003, Andrei Leitão wrote:
> The output and restrt files format are O.K. although I
> noticed a message in the output archive:
> check COM velocity, temp: 0.000000 0.00(Removed)
> I would like to know if there was any problem during my
> dynamic or if my protocol is wrong because I did not see it
> before.

This is just information, indicating that there is no center-of-mass (COM)
velocity -- that is fine.

> I tried to do a molecular dynamic with a micromolecule
> (and after that I will perform another one including the
> DNA) and AMBER did not understand my input pdb file when I
> used the Xleap program to generate the inpcrd and prmtop
> files.

For non macromolecules, you have to use LEaP (or antechamber) to prepare
descriptions of the molecules -- you can't just read in a pdb file. Once
you have the libraries prepared, it should not be a problem to read in
a pdb file with both a protein and a ligand (say). We would need more details
to provide further assistance.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Tue Jul 01 2003 - 18:53:01 PDT
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