[gmx-users] Please help

[Raj Badhan]

Hi all,
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).
Cheers

Raj Badhan
Postgraduate researcher
School of Pharmacy and Pharmacetical Science
The University of Manchester
Manchester, UK.