[gmx-users] coenzyme-protein complex

Justin Lemkul jalemkul at vt.edu
Mon Jan 6 15:02:17 CET 2014

On 1/6/14, 5:35 AM, Mostafa Javaheri wrote:
> ​Dear Gromacs users
> I would be grateful if any one answers my questions
> 1.
>   I have two coenzyme (GTP & GDP) and two Ion (Mg) attached to the
> hetrodimer protein, I am going to use charmm27 force field for Gromacs simulation and swissparam for achieving the ligands topologies; Could I trust at these topology (.itp) or they need
> some charge correction like PRODRG outputs?

That depends on the quality of the output charges.  SwissParam, to my knowledge, 
does not score the quality of the topology itself, though validation was done 
based on reproducing binding energies in the original paper.  That does not (in 
my opinion) necessarily guarantee that any topology it produces will be of high 

The ParamChem server provides a more quantitative score of the quality of the 
topology.  The larger the penalty score, the more refinement you need to do. 
The procedure for improving the topology is published and is also written as a 
web tutorial.  The other benefit of ParamChem is that it has recently been 
updated to the latest version of the CGenFF parameter set (2b8) and is thus 
up-to-date with the latest CHARMM force fields (with CHARMM36 representing 
improvements over CHARMM27).

> 2. Does anyone have ".mdp" fiels that consist with my system?

CHARMM parameters have been discussed extensively across the list.  The settings 
are dependent upon the force field, not the contents of the coordinate file.

> 3. I merged these two ligands into one mol2 file and
> sent it to the swissparam, then followed the rest of steps, is this OK or
> should I send them separately?

They should probably be treated individually.



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


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