[gmx-users] Problems with pdb2gmx and grompp

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Fri May 5 02:26:44 CEST 2006

>Always having the very same problem using pdb2gmx (in order to generate
the .ndx, .gro and .top files),
>it complained about not finding neither DPP nor DPPC in the residues
library. To solve this problem I

The problem is that the residue is not in the residue library, as the
error states.  And the residue library is stored in the rtp file.

You only use pdb2gmx when you have a protein like molecule with residues
linked together in some chain which you need to generate the topology
for, and they have to have entries in the database.  Typically the .rtp
file only contains residues for building proteins.  When you are working
with lipids, as you are here, you don't use that script since you
already have all the .itp, .top, .gro files etc required to run the
simulation.  Simply skip that step all together.

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 9524
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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