Dallas B. Warren wrote: > Gavin, > > >> I am performing the md on glutathione s-transferase bound to >> ethacrine. I was trying to use 'option 0' within pdb2gmx. I >> received an error concerning GTT. This is glutathione which >> is not represented in the Gff file. > > All gobbledegook to me. I ain't a protein person ;-) > >> I extracted the co-ords. from my pdb. This gave me the >> glutahione pdb, from which I generated the topology using prodrg. > > Take care with what forcefield you are using (i.e. option 0, don't know > what it is now, but used to be ffgmx which is a ff that shouldn't be > used for any research work, there are more developed and superior ones > to that one, see the emailing list for more discussion on that). Is it > one that is applicable for the system you are simulated? Is the > parameters you got via prodrg compatable i.e. the same forcefield? > >> Now, do I need to make a .rtp entry for this to enable me to >> use pdb2gmx for the transferase? If so, what's the easiest >> way? Thanks. > > If there is one residue within your protein and you don't have to use it > again some time down the track on another protein, then you can simply > use the .itp file generated by prodrg and include it (using the include > command) in your topology file. > > If there are more than one and any proteins down the track will also use > that same residue, then may be better to generate a rtp file entry to > make things faster/easier for you in the future. > > I would recommend you search this emailing list, there are a number of > discussions by those much more in the know than me on this topic. > > Hope that is of some assistance. > > Catch ya, > > Dr. Dallas Warren > Lecturer > Department of Pharmaceutical Biology and Pharmacology > Victorian College of Pharmacy, Monash University > 381 Royal Parade, Parkville VIC 3010 > [EMAIL PROTECTED] > +61 3 9903 9524 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble > a nail. > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Thanks Dallas You have cleared-up all my is residue troubles. All the protin is an organic acid polymer. However, the glutathione residue is critical, unfortunately. Gavin.
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