> On Oct 4, 2018, at 8:30 AM, Paul Buscemi wrote:
>
>
>
> Maria
>
> Regarding PVDF ( in 54a7 ff) here is some information that may be useful:
> === Input command to generate a 15 mer ===
> gb@RGB ~/Desktop/PVDF $ gmx x2top -f pdb/PVDF15.pdb -o pvdf.top -f
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 bon
Maria,
The procedure you are using is very much like I use. While I use 54a7 ff you
most likely are not but I know the procedure works with oplsaa.ft.
In using 54a7ff, I can use ATB to build a small version of the polymer - say
50 atoms or less --. ATB has problems with polymers over about 3
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 resu
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
