On 9/25/12 5:02 PM, Elie M wrote:
Thanks for your reply. I guess either way (x2top or pdb2gmx), I have problems.
pdb2gmx is giving the same old error residue 'UNK' is not found in topology
residue file whereas strangely enough x2top did not complain and was able to
assign topologies for 73 atoms out of 94 so maybe it is easier to use x2top
because in the other case I have to change files and I have no experience in
this whatsoever and I am really tight on time. What do you personally think?
Neither tool is guaranteed to produce a topology for an arbitrary molecule. If
g_x2top does not have the right parameters, it will fail. If pdb2gmx does not
have the right parameters, it will fail. g_x2top further assumes that some
generic set of atom types and functional groups will address whatever it is that
you're working with. Sometimes that's appropriate, sometimes it's not. Either
way, you're going to have to modify either the .n2t file or the .rtp file for
your chosen force field. Regardless of the route you choose, you're going to
have to come up with parameters for your molecule and learn how these files work
so you can modify them. Parameterization is an expert topic for a reason.
-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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