[gmx-users] topology problem with x2top

Dallas Warren dallas.warren at monash.edu
Thu Oct 4 03:48:54 CEST 2018

Sorry, can't help you directly, but can you post some of the commands
that you've actually run (copy and paste the exact lines), then the
error messages that you get (again a direct copy and past).  Be as
specific as you can be, including the different things you have
attempted to use, and the results.

The more exact details you give, the more able people are to help.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Wed, 3 Oct 2018 at 19:32, Maria Luisa <ml.perrotta at itm.cnr.it> wrote:
> Dear users,
> I need help. I want to build the topology of a polymeric chain of PVDF of
> 602 atoms, and of a sheet of Graphene Oxide of 202 atoms. I use the
> version of gromacs 5.1.4. The problem is that it does not recognize some
> atoms in the polymeric chain, and not at all the graphene oxide atoms. I
> already worked with the x2top command, I had already created another
> executable .n2t file, to complete the missing atoms in the atomname file,
> and in the past I built topology for graphene oxide and graphene systems,
> but now, all this command with my previous challenge doesn't t work. I'm
> doing a thousand tests but I do not know how to do it.
> I hope to get help.
> Thank you
> Maria Luisa Perrotta
> Ph.D Student, CNR-ITM
> via P.Bucci, 87036 Rende (Cs)
> Italy
> email: ml.perrotta at itm.cnr.it
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