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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