[gmx-users] using .pdb file from protein data bank

David spoel at xray.bmc.uu.se
Thu Jan 15 19:13:01 CET 2004

On Thu, 2004-01-15 at 19:03, Madhuri Agashe wrote:
> Hi,
> I want to use a pdb file from the protein data bank and run a MD simulation
> on it.
> How does gromacs treat the pdb file taken directly from the protein data
> bank? Are protonation sites checked or protonation/deprotonation done?
> How can I check the total charge on the protein before starting the
> silmulation?
just do the tutorial (demo first) and in the speptide example you can
get a quick start on your protein. For production you want to do some
changes (like use PME etc.)
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list