[gmx-users] Re: GROMACS-CYSTEINE PROTEASES
mutemibiochemistry at gmail.com
Sun Aug 25 17:35:25 CEST 2013
I am trying to minimize my ligand-protein structures but when I run the
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:
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.
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
>> 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
>> the two to make one PDB file that i can use as my starting structure for
> 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:
> 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
> gmx-users mailing list gmx-users at gromacs.org
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*MUSYOKA THOMMAS MUTEMI
Mob nos **+27844846540**
B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science
*PhD Student-Bioinformatics (Rhodes University)
*Skype ID- MUSYOKA THOMMAS MUTEMI
Alternative email - thommas at sia.co.ke
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