[gmx-users] rtp use

[Gavin Seddon]

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.
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> 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.
-------------- next part --------------
A non-text attachment was scrubbed...
Name: gavin.m.seddon.vcf
Type: text/x-vcard
Size: 231 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20061011/97f6b6ab/attachment.vcf>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 252 bytes
Desc: OpenPGP digital signature
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20061011/97f6b6ab/attachment.sig>