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I would like to thank everyone for their help. Several individuals responded
to my initial post.<br>The consensus seemed to be to use distance restraints.
My question is, because distance restraints<br>creates penalties if the
distance between two atoms EXCEEDS UPPER BOUNDS, wouldn't that apply more for
pulling<br>two terminal atoms apart? In example, as the peptide is being pulled
apart, if the distance exceeded a certain<br>value, a penalty would be assessed
to the force. In my simulation, with the terminal ends coming together,
how<br>UPPER bounds be set? Would I set my upper bounds very low (i.e. - 0.5
nm range)? This way, even the starting<br>structure, with the distance between
the terminal ends starting at ~3.5 nm, would be assessed a penalty.
Another<br>idea suggested by the GROMACS manual was to incorporate a [bonds]
type 6 exclusion in the topology, to create a<br>harmonic potential between the
two atoms. Would this serve to help bring the two ends together during
simulation?<br>Again, much thanks to those who
responded.<br><br>--Venk<br><br><br>VENKATESH HARIHARAN wrote:<br>>>
Hello All,<br>>> <br>>> First, for this question I am referring to
GROMACS 3.3.3. I have <br>>> thoroughly read the archives for errors on
why a simulation box might <br>>> explode. My simulations require that I
bring the N and C terminal ends <br>>> of a ~20 amino acid peptide as
close together as possible. To do this, <br>>> I am using the pull code
to freeze the C terminus and pull the N <br>>> Terminus toward
it.<br><br>>I would use normal MD with distance restraints between suitable
terminal <br>>atoms. This is a much simpler approach to this
problem.<br><br>>> I keep getting the following error during the
<br>>> simulation:<br>>> <br>>> Back Off! I just backed up
md_traj.xtc to ./#md_traj.xtc.1#<br>>> Warning: 1-4 interaction between 5
and 10 at distance 1.480 which is <br>>> larger than the 1-4 table size
1.000 nm<br>>> These are ignored for the rest of the
simulation<br>>> This usually means your system is exploding,<br>>>
if not, you should increase table-extension in your mdp file<br><br>>See <a
target="_new"
href="http://wiki.gromacs.org/index.php/blowing_up">http://wiki.gromacs.org/index.php/blowing_up</a><br><br>>> My question: Is there any way to completely ignore this error, so that <br>>> the N Terminus is pulled as close as possible to the C Terminus?<br><br>>That's not your problem. Atoms 5 and 10 are too close because there's <br>>something unphysical about your model, and anyway these atoms are not <br>>your terminal pair.<br><br>>> I <br>>> understand that the results in the .pdo file of the pull simulation may <br>>> be unrealistic, but I simply need to get a peptide structure whose N and <br>>> C Terminal ends are close together (within .5 nm). On a side note, are <br>>> there any suggestions for respectable molecular modeling software with <br>>> which I may be able to BUILD a circular peptide (i.e. - N and C Terminal <br>>> ends are brought close together)? Any help is appreciated.<br><br>>There a!
re a few links here <br>><a target="_new" href="http://wiki.gromacs.org/index.php/Coordinate_File">http://wiki.gromacs.org/index.php/Coordinate_File</a> that might help.<br><br>>Mark<br></pre>______________________________<br><br>Venkatesh Hariharan<br>The Pennsylvania State University<br>Schreyer Honors College<br>Undergraduate - Bioengineering<br><br>"You must be the change you wish to see in the world."<br>--Mohandas Karamchand Gandhi<br><br><br></div>