[gmx-users] Re:Re: x2top

[Justin A. Lemkul]

Bernhard Knapp wrote:
>  > 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... 

Well, generating a PRODRG topology for a protein is useless too, since probably 
none of the parameters are going to be quite right.  Use PRODRG for just the 
sugar ligand.  If you have specific problems (error messages) that arise from 
doing that, it is much easier to diagnose.

Furthermore, there is an excellent tutorial written by John Kerrigan for an 
enzyme-inhibitor complex that you can find with Google, and it may even be 
linked on the wiki site.

-Justin

> 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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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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