Justin Lemkul jalemkul at vt.edu
Wed Aug 21 22:17:01 CEST 2013

On 8/21/13 4:00 PM, MUSYOKA THOMMAS wrote:
> Dear users,
> I am new to GROMACS and i have just been practising with several tutorials.
> I am trying to do a molecular dynamics simulation of cysteine proteases an
> example falcipain-2 (PDBID=2OUL) and got several issues to pose
> 1) looking at the structure it has water molecules - do i get rid of the
> water molecules before starting the whole process

If they are functionally relevant, leave them alone.  If not, it doesn't really 

> 2) when i generate the topology file, i get several .itp files
> corresponding to each chain. Which one do i use for subsequent steps?

All of them.  The .top written by pdb2gmx handles everything for you.

> 3) How do i handle the presence of disulphide bonds and salt bridges in my
> MD simulation process?

Disulfide bonds either exist or they don't, as defined by pdb2gmx.  You can 
control which ones exist with the -ss option.  I don't know what you want to do 
about salt bridges; there is no specific topological definition for them and 
they will likely break and form during the simulation according to how favorable 
their interactions are.



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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