Dear Justin, Thanks so much. If get stuck i will come knocking on your door.
Cheers. On Wed, Aug 21, 2013 at 10:17 PM, Justin Lemkul <jalem...@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@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- *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 - thom...@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. * -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
