Luke Pestl wrote:
Hi,
I am new to gromacs and I am trying to model a system that has a protein
and a fairly large and complex random polymer. I am having trouble
adding the polymer to the system. PRODRG was useful with a small
segment of the polymer, but I would like to use a much larger molecule.
I thought I could enter the monomers into the rtp file, but because it
is randomly branched and cross linked I do not know if this is
possible. The description of x2top sounded hopefull, and I thought that
it might be able to generate an rtp entry for me, but I cannot get the
program to work because I cannot find the n2t library files that it
requires (am I supposed to make these files, or should they have been in
the package somewhere?).
Any suggestions as to how I should proceed would be greatly appreciated.
The intrinsic irregularity of your structure will require you to build
structure by hand - or at least to write your own scripts to build them.
You should build them out of structural monomers whose topologies are
defined in an .rtp file and get pdb2gmx to generate the topology for
each such molecule, in the same way that it works for amino acid
polymers. Depending on your polymer, you will probably need to build
your monomer topologies by hand in the .rtp file, by analogy.
Mark
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
