[gmx-users] Simulation in Constant pH simulation ...

[Justin Lemkul]

On 6/15/16 11:49 AM, Nikhil Maroli wrote:
> Hi,
> Justin , thanks for your reply.
> Actually, my system is cyclic peptide nanotube in water,which I made using
> charmm-gui. Protonation option availbe  in " PDB reader " but how to
> confirm the pH,based on protonation ? or is it possbile to make any

You don't "confirm the pH" because there is none.  You don't have titratable 
sites and you don't have H3O+ floating around.  The point of a fixed-charge 
simulation is to simulate the dominant protonation state that would be found at 
a given pH in a real, physical system.  The protonation states are chosen based 
on pKa values of those titratable moieties and which form will dominate at a 
given pH.

> changed after getting the out put
>

I wouldn't try to make post-hoc changes.  Adding or deleting H atoms will change 
everything about the topology.  Set it up properly to start.

-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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