VENKATESH HARIHARAN wrote:
Hello All,
First, for this question I am referring to GROMACS 3.3.3. I have
thoroughly read the archives for errors on why a simulation box might
explode. My simulations require that I bring the N and C terminal ends
of a ~20 amino acid peptide as close together as possible. To do this,
I am using the pull code to freeze the C terminus and pull the N
Terminus toward it. I keep getting the following error during the
simulation:
Back Off! I just backed up md_traj.xtc to ./#md_traj.xtc.1#
Warning: 1-4 interaction between 5 and 10 at distance 1.480 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
My question: Is there any way to completely ignore this error, so that
the N Terminus is pulled as close as possible to the C Terminus? I
understand that the results in the .pdo file of the pull simulation may
be unrealistic, but I simply need to get a peptide structure whose N and
C Terminal ends are close together (within .5 nm). On a side note, are
there any suggestions for respectable molecular modeling software with
which I may be able to BUILD a circular peptide (i.e. - N and C Terminal
ends are brought close together)? Any help is appreciated.
This type of error should not be ignored. It means there is something
physically unrealistic about your system. Either you are pulling too fast or
somehow incorrectly, or the parameters you are otherwise using are incompatible
with the procedure.
Have you considered using distance restraints instead?
-Justin
______________________________
Venkatesh Hariharan
The Pennsylvania State University
Schreyer Honors College
Undergraduate - Bioengineering
"You must be the change you wish to see in the world."
--Mohandas Karamchand Gandhi
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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