[gmx-users] free energy calculations for reference state for constant pH MD simulations...

[Justin Lemkul]

On 2/10/14, 2:48 PM, Mehmet Ozbil wrote:
> Now I successfully ( I believed so) incorporated both protonated and
> deprotonated states of GLU residue in the .top file. As I am trying to
> energy minimize the system, it gives me an error saying:
>
>
> WARNING 1 [file GLUTest3_GROMOS_p.top, line 52]:
>    Some parameters for bonded interaction involving perturbed atoms are
>    specified explicitly in state A, but not B - copying A to B
>
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> turning H bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'LIG'
> turning H bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning H bonds into constraints...
> Coupling 1 copies of molecule type 'Protein_chain_A'
>
> NOTE 1 [file GLUTest3_GROMOS_p.top, line 141]:
>    State B has non-zero total charge: -3.770292e-04
>
>
> What do they mean? What shall I do regarding the non zero charge and more
> importantly the missing interactions in state B?
>

On line 52, you have a problem where an atom type is changing but a bonded 
interaction in which it is involved is not changing.  By default, grompp simply 
applies the A-state parameters in such a case, but it's probably wrong.

The charge is also a problem.  A value of that magnitude is not generally 
negligible and suggests a problem with the topology.

-Justin

-- 
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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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