[gmx-users] Please help
r.k.badhan at stud.man.ac.uk
Wed Dec 3 15:14:00 CET 2003
I would appreciate any help or assistance anyone can offer. This is
a very novice question, but its driving me mad!
I keep getting LINCS error on my system before it begins a PR md
simulation (i.e. -0.004ps, -0.002 ps etc..).
My system is a protein dimer with a ligand placed in between the
two in the approx binind site.
After solvating the system and initiating the PR commands, the
programs halts with LINCS errors that appear to be due to the
bonds within the ligand.
Now, in John Kerrigans tutorial, there is no mention of constraints
on the actual ligand, but in the user archive I've seen people doing
various things with adding position contraints to the bonds within
their ligands. I've tried a few things that people have done, and still
am getting nowhere.
I would appreciate any assistance in sorting this out
(I have my ligand, with the relevant ITP files from PRODRG and the
posre itp file using genpr).
School of Pharmacy and Pharmacetical Science
The University of Manchester
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