[gmx-users] add. residue in topology database

[Daniele Veclani]

Thank you Justin.

2015-03-11 12:33 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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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