Dallas B. Warren wrote: > Gavin, > >> I have created my topology file but when I run pdb2gmx it >> complains of a missing rtp file. Will someone outline how I >> use pdb2gmx when the topology for my protein is not in the >> top dir? Gavin > > You don't. > > pdb2gmx only works when the forcefield that you selected has the > residues making up the protein within it's (or the files provided with > GROMACS) database. > > If you have some unusual residues or a forcefield that hasn't had the > appropriate residues added to the DB, then it wont work and will fail > with an error saying something about unknown residues. > > It may be a residue naming problem, with the names provided within the > pdb file you are using being incorrect. So change them to the correct > ones and it may work. > > If it is just one or two residues missing, then you can add them to the > rtp file, with the appropriate parameters etc. > > If more substantial, then you need to look at generating your own > topology files, which is covered in the manual and in a significant > number of emails on this emailing list. All of the above are also > covered in detail too. > > 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
Dear Dallas, Thanks for your help. I am new to Gromacs so I didn't want to give an impression that I am familiar with Gromacs. 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. I extracted the co-ords. from my pdb. This gave me the glutahione pdb, from which I generated the topology using prodrg. 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. Gavin.
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