[EMAIL PROTECTED] wrote:
dear gromacs user
i am doing simulation of Gal1p protein with ligand and without ligand.i
made the system without ligand by removing the ligand from pdb file then i
use pdb2gmx for generating topology file and editconf for adding box
dimention and add spc water molecules.i have not face any problem up to
grompp but when i did energy minimization of system i got this warning:-
"Warning: 1-4 interaction between 2779 and 2788 at distance 1.005 which is
larger than the 1-4 table size 1.000 nm
These 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"
but em is comleted with machine precession with -ve energy,
Hmm? If you got this warning during EM, it seems most unlikely you'd
converge that EM, or that you should trust the resulting structure to be
a minimum.
i added
table-extention (1.1nm)in mdp file, and got same warning.even i don't what
affect done on system by adding table-extention.I am also getting same
problem with ligand.kidnely help me
sanjay
Justin's advice last time still applies... see
http://www.gromacs.org/pipermail/gmx-users/2008-May/034017.html This
kind of error arises in EM because you have some serious problem with
your starting structure, topology or both. Visualize your starting
structure, and/or along the EM "trajectory" to see which part of your
structure is causing the problem when. Atoms 2779 and 2788 are a good
start, but they might be the symptom and not the cause.
Mark
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