[gmx-users] Re: gmx-users Digest, Vol 52, Issue 96

Justin A. Lemkul jalemkul at vt.edu
Sat Aug 23 21:35:26 CEST 2008

Ragnarok sdf wrote:

> Tahnk you Justein for the reply.
> I read again chapter 5, this time I tried to be more thorough, but still 
> I don't really understand why my topology is coming out bad. My .itp 
> files do not look like the one from the manual abou UREA. What i mean 
> is, the angles and bonds parts of the file have only 3 columns. Although 
> I read the manual, I am still not sure about the real problem here.

There is no problem with only having three or four columns, per se.  Amber 
topologies will be shown as such.  The bonded parameters will be read from the 
ffamber*bon.itp file.  Have you identified the atoms involved in the problematic 
bond(s) and angle(s)?

> You mentioned that each residue should end up with an integer charge. 
> Well, mine don't.
> What exactly do you mean with "post one of your nucleotides here"? From 
> my pdb file or from my itp generated files? The entire double helix with 
> all nucleotides or really just one of them?

Post a single nucleotide from the topology.  Sorry if I wasn't clear.  What 
would be interesting to see is what charges and atom types you've been assigning 
to each nucleotide.

> Sorry for asking these details. But I just want to make sure I don't 
> waste your time with useless posts.

Much appreciated :)


> Thank you again
> And thank you in advance
> Fabrício
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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