[gmx-users] "DPC" not found in residue topology database

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Fri Jul 21 02:17:26 CEST 2006

>I would start a dynamical study with DPC micelles and peptides, but the
DPC is not
>mentioned in topology database.I  imported the dpc.itp file in
/usr/local/gromacs/share/gromacs/top/ ,
> but this is not enough: in fact, when I start converting the pdb file,
I find the error "DPC
>not found in residue topology database". Can you suggest me a procedure
to  upload Gromacs
>topology database with a new molecule?

pdb2gmx is only used when you have molecule(s) that are within the
database for that pariticular forcefield you select.  Plus it is really
meant to be used for things like proteins or other long chain things
that have lots of residues/components that make it up.  It makes
generating the topology files simple.

In your case, when the molecule isn't part of the database, and it is a
single molecule that isn't linked up with others, then you simply skip
the whole pdb2gmx step and either use the topology files you have found
somewhere else, or generate some yourself by hand or using prodrg.

Note, when you get an error message, also a good idea to search the
emailing list for responses / threads about that sort of error.  There
is a lot of messages in the database, and majority of errors have
solutions for them in it already.

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. 

More information about the gromacs.org_gmx-users mailing list