[gmx-users] rtp use

[Dallas B. Warren]

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
dallas.warren at vcp.monash.edu.au
+61 3 9903 9524
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
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