[gmx-users] topology problem with x2top

[Maria Luisa]

Dear Dallas the command are:
FOR PVDF
gmx x2top -f PVDF_chain.gro -o PVDF_chain.top -ff oplsaa -name

the system gives me this lines:

Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t

There are 23 names to type translations in file oplsaa.ff

Generating bonds from distances...

atom 44

Can not find forcefield for atom C21-2 with 3 bonds

Can not find forcefield for atom C18-5 with 3 bonds

Can not find forcefield for atom C16-10 with 3 bonds

etc etc
Fatal error:

Could only find a forcefield type for 302 out of 602 atoms

The same thing happens with graphene oxide. The problem is that I built in
the past combined systems of these two molecules, without problems. I
created an executable n2t file as I mentioned in the previous post.

Maria Luisa
Thank you for your help


> 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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Maria Luisa Perrotta
Ph.D Student, CNR-ITM
via P.Bucci, 87036 Rende (Cs)
Italy
email: ml.perrotta at itm.cnr.it