On Tue, Nov 26, 2013 at 8:08 AM, sunita gupta <sunita....@gmail.com> wrote:

> Thanks Justin,
> Its strange that some atomtypes like ha, h1, n2 etc whose parameters are
> already present in the gbsa.itp are also not recognised.
> I have many more ligands to deal with. Can you tell me how to overcome this
> issue, or whats the possibility of doing implicit simulation of
> protein-ligand complexes with gromacs

You need to list all of the atomtypes you are using within
[implicit_genborn_params], and I believe they are case-sensitive so h1 and
H1 are not the same. If the ligand h1 is actually the same as the force
field's H1, then just use H1 and save yourself the trouble.




Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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