[gmx-users] error with x2top.

[Justin Lemkul]

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

-- 
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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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