[gmx-users] Re: GROMACS-CYSTEINE PROTEASES

[MUSYOKA THOMMAS]

Hello,
I am trying to minimize my ligand-protein structures but when I run the
code,
 mdrun -v deffnm em.tpr
i am getting the error:

Program mdrun, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/gmxfio.c, line: 519

Can not open file:
topol.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
 Any one with any solution to get through this.
Thank you



On Thu, Aug 22, 2013 at 10:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/22/13 3:25 PM, MUSYOKA THOMMAS wrote:
>
>> 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<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?
>>
>>
> You need to do background reading about the enzyme, its mechanism, and the
> specific structure that you are using.
>
> I removed the waters from lysozyme for that tutorial to avoid confusion
> that would undoubtedly arise from multiple SOL entries after genbox and
> then the choice of group for embedding ions.  In general, one should not
> necessarily dismiss crystal waters.  There's probably never any harm in
> keeping them.
>
>
>  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?
>>
>>
> If you've done docking, you already have it.  The coordinate file is not
> the challenge, the topology is.  Deriving parameters for an arbitrary small
> molecule for an existing parent force field is an advanced topic, one that
> can require weeks or months of work.  You will have to invest considerable
> time reading about the underlying theory of your chosen force field and how
> one goes about deriving new parameters.
>
> As for dealing with the complex itself, there's a tutorial for that:
>
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
> gmx-tutorials/complex/index.**html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html>
>
>
> -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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-- 
*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
*

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