[gmx-users] add. residue in topology database

[Justin Lemkul]

On 3/11/15 6:22 AM, Daniele Veclani wrote:
> Dear users
>
> I'm trying to build the topology files for a box with 1000 molecules of
> water and an organic molecule.
>
> when I use pdb2gmx come out the error: "OUB7 not found in residue topology
> database"
>
> how do I put this residue in the database?
>
> I have a .itp file for this molecule.
>

If you have an .itp file, you don't need pdb2gmx at all.  The topology for an 
organic molecule in water is trivially simple:

#include (parent force field)
#include water_model.itp
#include organic_molecule.itp

[ system ]
whatever

[ molecules ]
organic 1
water   N

If you want to add it to the .rtp, see 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field 
but you'll just be investing a lot of unnecessary time when the above approach 
takes a few moments in a text editor.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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