On 5/11/15 2:24 PM, MPI wrote:
Dear Users,
I prepared ligand topologies by two different methods, one with
Acpype and the other with Prodrg.
It is sad that independent simulations give the same (or similar)
numerous Lincs warnings and the system blew up at the end.
Errors look like
LINCS WARNING relative constraint deviation after LINCS:
rms 0.019243, max 0.893307 (between atoms 2073 and 2121)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2073 2121 90.0 0.1758 0.1844 0.0974
Wrote pdb files with previous and current coordinates
I was able to trace down errors that came mainly from the "bad" atom
indexed 2073, which is an Oxygen in a gro file like
131DRG O3 2073 1.789 5.047 4.061
131DRG H45 2121 1.701 5.076 4.032
I suspect atom 2121 is a polar H and it should be deprotonated or
removed ??? or did I miss something ? but the question is how to
prepare this ligand topology without causing LINCS warnings.
Hacking off atoms because the simulation fails is a pretty bad strategy :)
Please also see attached ligand coordinates. This ligand is called
Cholesterol-Sulfate.
General strategy for diagnosing situations like this is found in
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
Simplify the system. Work scientifically!
It could also be a problem with your protocol and/or .mdp files, but only by
systematically investigating what's going on will you figure out what the
problem is.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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