On 10/4/12 4:22 PM, Elie M wrote:
I guess now I get what is happening finally. Correct me if I am wrong. The
.top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which
was also modified to include atoms that were not there *but present in
atomtypes.atp). The .top file describes all the bonds and angles in the
molecule. This was successful. However the characteristics of some of those
bonds are not described in the foplssabon.itp file; for example I have Sulfur
in my molecule connected to carbon which has no entry in foplsaabon.itp and
must be added to that file manually. I guess now I am in a position to check
those bonds and add the relevant information which i will gather maybe from
HYPERCHEM or ARGUSLAB??....A final question is in order here: what do the
You will have to calculate reasonable values in some way, yes.
parameters (b0, kb), (th0, cth), (q0,cq), and (phi0, cp,mult) represent and
in what units?
All of this is in the manual.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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