MUSYOKA THOMMAS mutemibiochemistry at gmail.com
Wed Aug 21 22:31:04 CEST 2013

Dear Justin,
Thanks so much. If get stuck i will come knocking on your door.


On Wed, Aug 21, 2013 at 10:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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 matter.
>  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
> --
> ==============================**====================
> 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 <jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> ==============================**====================
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Mob nos **+27844846540**
B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science
(Nagasaki University)*
*PhD Student-Bioinformatics (Rhodes University)
Alternative email - thommas at sia.co.ke

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