[gmx-users] rtp use

Gavin Seddon gavin.m.seddon at manchester.ac.uk
Wed Oct 11 05:51:59 CEST 2006

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
> 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
> a nail.
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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

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?

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