[gmx-users] a quick question (forgot to ask).

[Elie M]

Sorry one more thing: For one of the atoms S that x2top did not assign the topology it said 0 bonds although S is a part of the Thiophene molecule  which is connected to two carbons..what does it mean "0 bonds"?

Thanks 

> From: elie.moujaes at hotmail.co.uk
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] error with x2top.
> Date: Tue, 25 Sep 2012 22:17:21 +0100
> 
> 
> Yep You are right. I will try my best to change the files accordingly.
> Thanks 
> 
> > Date: Tue, 25 Sep 2012 17:05:20 -0400
> > From: jalemkul at vt.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] error with x2top.
> > 
> > 
> > 
> > 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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