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 gmx-users@gromacs.org 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
