[gmx-users] Automating pdb2gmx

Justin Lemkul jalemkul at vt.edu
Wed Nov 4 02:31:10 CET 2015

On 11/3/15 8:17 PM, Jernej Zidar wrote:
> Hi,
>    I would like to import several hundred molecules to Gromacs.
>    I know that one can set the force field "automatically" and pick the
> desired water model like so:
> echo 16 | pdb2gmx -f some.pdb -water spc
>    Is there a way to automate the selection of the termini? The proteins I
> am importing have no termini, i.e. when prompted I have to pick "3" for
> both N- and C-terminals of both chains, however I can't see an option to do
> that "automatically".
>    Any tips on how to do that?

You can echo as many selections as you need.  Alternative approaches are also 
shown at http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list