[gmx-users] problem in defining protonation state of amino acids

[Justin Lemkul]

On 3/13/15 8:08 AM, Tushar Ranjan Moharana wrote:
> Hi everyone,
> I want to do a constant pH simulation of my protein using CHARMM36. I

Just for clarity "fixed protonation" and "constant pH" are not synonymous. 
Natively, GROMACS does not do constant pH simulations, though I believe some 
groups have developed software to do this.

> calculated protonation state of various amino acid at required pH using H++
> server. However when trying to run pdb2gmx got fatal error "Atom HB3 in
> residue SER 3 was not found in rtp entry SER with 11 atoms while sorting
> atoms". I can remove the error by adding -ignh but my concerned is this may
> change the protonation state. Please help me with your valuable
> suggestion.

As the name implies, HB3 is attached to CB.  The force field expects HB1 and 
HB2, but your coordinate file doesn't adhere to that nomenclature.  Renaming the 
offending HB3 or using -ignh are both fine.  HB* are not titratable (under 
normal circumstances, and moreover the force field won't support any weird 
anionic CB form of SER) so they don't factor into your setup.

-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

==================================================