[gmx-users] Re: GROMACS-CYSTEINE PROTEASES

[MUSYOKA THOMMAS]

Dear users,
I am dealing with molecular docking of ligands to cysteine proteases and i
got several questions to pose.
1) For example looking at the structure of Falcipain-2 (PDBID=2OUL), i can
see it got several water molecules. when and how do i determine whether i
should stripe off the molecules. According to
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html,
i should check if the the catalytic site has water molecules. How do i
determine this?

2) I got a cysteine PDB structure and a docked ligand PDB. How do i combine
the two to make one PDB file that i can use as my starting structure for MD
simulations?

Thanks.



On Wed, Aug 21, 2013 at 10:00 PM, MUSYOKA THOMMAS <
mutemibiochemistry at gmail.com> 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
> 2) when i generate the topology file, i get several .itp files
> corresponding to each chain. Which one do i use for subsequent steps?
> 3) How do i handle the presence of disulphide bonds and salt bridges in my
> MD simulation process?
> 4) i will be glad if anyone grants me a tutorial which can help me in this.
>
> Thank you.
>
> --
> *MUSYOKA THOMMAS MUTEMI**
> B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science
> (Nagasaki University)*
> *PhD Student-Bioinformatics (Rhodes University)
> *Skype ID- MUSYOKA THOMMAS MUTEMI
> Alternative email - thommas at sia.co.ke
> *
>
> "Do all the good you can,
> By all the means you can,
> In all the ways you can,
> In all the places you can,
> At all the times you can,
> To all the people you can,
> As long as ever you can."
>
> - John Wesley.
> *
>
>


-- 
*MUSYOKA THOMMAS MUTEMI
Mob nos **+27844846540**
B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science
(Nagasaki University)*
*PhD Student-Bioinformatics (Rhodes University)
*Skype ID- MUSYOKA THOMMAS MUTEMI
Alternative email - thommas at sia.co.ke
*

"Do all the good you can,
By all the means you can,
In all the ways you can,
In all the places you can,
At all the times you can,
To all the people you can,
As long as ever you can."

- John Wesley.
*