C Johnson wrote:
"""
This depends entirely upon what your goal is. Your original question implied
you wished to build a system of multiple, identical peptides, pertaining to:
http://www.gromacs.org/Documentation/How-tos/Multiple_Chains#Identical_chains
Now you want a multimeric protein for which there are multiple, potentially
different peptide, i.e.:
http://www.gromacs.org/Documentation/How-tos/Multiple_Chains#Non-identical_chains
The approaches are completely different, as the documentation should make quite
clear. Simply "having multiple chains" is a very vague statement. Perhaps if
you clearly stated your goal for the simulation I (or someone else) could help
you better.
As for the PDB site, there are probably thousands of proteins in line with what
you want. Any heteromultimeric protein would do (assuming, of course, the
latter case of non-identical chains).
-Justin
"""
Sorry I wasn't clear. Basically I want to have a simulation box with as many
of the same polypeptide as I can cram in, essentially a simulation of the
polypeptide melted.
I would like to see how the polypeptides interact with each other with the
ultimate goal of simulating block copolymers. Since I'm new with Gromacs, I'm
just trying
to figure out how to run simulations with multiple chains where all chains are
the same type.
Then I doubt anything you download from the PDB would be very helpful. You have
topologically identical chains that are not all going to be processed by
pdb2gmx. What you need to do is generate coordinates for your (identical)
peptides in some way that makes sense. You can do this with genconf (applying
-nbox and/or -maxrot as necessary), editconf (manually centering and/or
translating your peptides to obtain the desired configuration), or perhaps even
genbox (with -ci and -nmol options). Once you have constructed a suitable
system, then and only then should you modify the topology (to reflect the number
of peptides present) and proceed.
You will have to experiment a bit to decide which approach is best for your
needs.
Justin, you've been very helpful so far and I appreciate it.
Happy to help.
-Justin
--
========================================
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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