[gmx-users] Ligand-Ligand interaction

[Justin A. Lemkul]

Hovakim Grabski wrote:
> 
> I have been trying to set up simulation between 10 molecules of taurine 
> with lysolecithin stearoyl, i generated the topology files with PRODRG 
> but i s haven't managed to run the equilibrium. The error i recieve says 
> there's a problem with the position restrain files.
> What can i do?

Without the exact error message, it's hard to help.  Likely you've constructed 
the topology incorrectly.  See the following:

http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

Also note that PRODRG topologies are generally unreliable and require careful 
reparameterization.  See the paper linked from:

http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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