[gmx-users] Md simulation error

[Justin Lemkul]

On 10/29/16 5:04 AM, maria khan wrote:
> Thanks  alot  Justin A. Lemkulfor your strong concern.
> can you please guide me in conforming protonation states for residues.im
> new user of gromacs for simulation.

Start with some basic tutorials that show you how everything works in good systems.

Then consult the manual about what the force field files contain and what they 
do, particularly the .rtp files, which define required residue nomenclature. 
Then you will see how your file does not conform to what the force field 
requires.  Of course, the simplest solution is to do what pdb2gmx says and use 
-ignh to have the H atoms rebuilt with the proper names.  Many programs and 
structural databases do not conform to standard nomenclature, which prevents 
pdb2gmx (or any topology-generating software, it's not like this is just a 
GROMACS problem) from working properly.

-Justin

-- 
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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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