[gmx-users] rtp use

Gavin Seddon gavin.m.seddon at manchester.ac.uk
Fri Oct 13 02:29:57 CEST 2006

Dallas B. Warren wrote:
> 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
> 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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Thanks Dallas
You have cleared-up all my is  residue troubles.
All the protin is an organic acid polymer.  However, the glutathione
residue is critical, unfortunately.
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