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<pre wrap=""><div class="moz-txt-sig">> Justin wrote:</div></pre>
<pre wrap="">> 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.
<font color="yellow" size="5">"ERRDRG> Too many atoms in this molecule (should be <=300).
PRODRG> Program terminated unsuccessfully, sorry!"
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<pre wrap=""><div class="moz-txt-sig">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:
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<pre wrap="">> 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. <div class="moz-txt-sig">
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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