abhijit kayal wrote:
Hello everybody,
I am going to simulate an enzyme complex taking
a ligand at active site and another ligand at allosteric site. When I
ran md simulation taking ligand at active site only then it was ok. But
when I am running the simulation taking both the ligand it is showing
error "1-4 interaction between 3481 and 3485 at distance 4.979 which is
larger than the 1-4 table size 2.000 nmThese are ignored for the rest of
the simulation.This usually means your system is exploding,if not, you
should increase table-extension in your mdp file or with user tables
increase the table size". When I look the particular atoms they
corrospond to the last atom of the ligand at the active site
and the fourth atom the ligand at the allosteric site. So I can not
understand why GROMACS takes into account bcause they are far apart or
is there any wrong to my pdb file. I am genereting the coordinate and
topology using PRODRG server. I am also attached my input pdb file.
Please help me to find out the problem.
Have you looked into the list archive? This "blowing up" error has been
reported, diagnosed, and solved hundreds (if not thousands) of times, and there
are only a few reasons why it's happening. Also:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
From your description, it sounds as if the topology is constructed incorrectly,
since your two separate ligands are being considered one molecule and thus
experiencing intramolecular 1-4 interactions. Also note (as I've said dozens of
times), face-value PRODRG topologies are often unsatisfactory (and thus
unreliable) without modification of charges and charge groups. See here:
http://www.gromacs.org/Documentation/How-tos/Parameterization
-Justin
Abhijit
--
========================================
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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