[gmx-users] First question.

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Thu Aug 4 05:10:33 CEST 2005

> I'm just getting started with gromacs. Here's what I'm trying 
> to do: I have a molecule in mdl .mol format and I want to use 
> it in the gmxdemo instead of the cpeptide.pdb. Clearly, I 
> have to convert it to PDB before I can do that. I used babel 
> to convert, it succeeds but it labels all the residues UNK. 
> This isn't really a problem, since I don't care about those 
> for this process anyhow, however, pdb2gmx dies fatally when 
> it sees UNK.
> Is there a way to make pdb2gmx ignore the UNK's or convert 
> directly from .mol to .gro?

The residue name is what pdb2gmx uses to built the topology of the
molecules.  So if it doesn't know what residue it is, then it can't
build the topology.  And those residues need to be known for the
particular forcefield you are using too.

Even if you convert your .mol file to .gro, where is your topology
file/data coming from?  Telling it how the atoms are bonded together,
bond constants, bond angles, dihedrals, electrostatics etc ....

You might be best off using the PRODRG server, which will take your
coordinate file and makes a topology for it, in a number of different
forcefields.  Depending on what the molecule is, there parameters may or
may not be any good.  But should be sufficient for you to go through
with the tutorial.

Catch ya,

Dr. Dallas Warren
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 9073
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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