[gmx-users] Re:Re: x2top

Bernhard Knapp bernhard.knapp at meduniwien.ac.at
Fri Nov 28 16:47:03 CET 2008

 > Justin wrote:

> It looks like your coordinate file is from 
> PRODRG; why not use PRODRG to generate a rough topology, and refine it according 
> to the ffG43a1 parameters?

The problem is that the sugar in in contact with a bigger protein complex and the PRODRG server is not willing to accept more than 300 atoms.

"ERRDRG> Too many atoms in this molecule (should be <=300).
PRODRG> Program terminated unsuccessfully, sorry!"

if i create the topology of the protein straigth forward with pdb2gmx 
and the sugar topology with PRODRG then gromacs is not happy about the 
merged file. if i just use the topology of the sugar without the protein 
then the simulations starts but the atoms are not moving during the 
simulation. they are exactly at the same position in frame 1 and frame 
n. therefore had the idea to use the build-in x2top function. so i would 
be glad to get it somehow working... > Tsjerk wrote:

> Why would you want to use the Gromos96 43a1 force field for this and
> why use x2top to provide the topology for it? As Justin said, you
> could use the PRODRG topology. 
It is more the problem to get the x2top function running with an 
arbitrary force field but none of them seems to work with my structure. 
cheers bernhard

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