[gmx-users] Ligand-Ligand interaction

2011-12-28 Thread Hovakim Grabski 


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?
Thanks in Advance

Hovakim Grabski
Russian-Armenian Slavonic University-- 
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Re: [gmx-users] Ligand-Ligand interaction

2011-12-28 Thread 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

--


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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