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: case.scripps.edu
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 | http://www.scripps.edu/case
==================================================================
Received on Tue Jul 01 2003 - 18:53:01 PDT
