Justin A. Lemkul wrote:
I can see how this rapidly becomes difficult :) I don't believe that
pdb2gmx can handle such "multi-directional" bonding, since the residues
that are connected are not necessarily numerically sequential.
I should amend this statement (typing quicker than the brain can keep up!) - It
is not that pdb2gmx cannot handle multi-directional bonding, it is moreso that I
don't think it cannot be done using the +/- convention of the .rtp files.
Using specbond.dat, as I suggested before, should be a viable alternative.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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