[gmx-users] ATB topology: itp to top conversion

[Mark Abraham]

Hi,

On Wed, Jun 14, 2017 at 1:07 AM Anna Lappala <lappala.anna at gmail.com> wrote:

> Dear all,
>
> I am confused: I have my pdb file as well as the itp file produced by ATB.
> I want to convert these into top and gro files but the molecule is not
> recognised by the forcefield when I do the following:
>
> pdb2gmx -f input.pdb -o output.gro -i topology.itp
>

pdb2gmx is mostly for matching stuff found in .rtp files to produce .itp
files. You already have your .itp file.


> I have looked through tutorials and on the mailing list, but mostly the
> workaround is to #include the itp file into an existing top file - which i
> do not have because i only have a heteromolecule, and no protein...
>

The .top files are intended to be edited and written, e.g.

#include "your.ff/forcefield.itp"
#include "heteromolecule.itp"
#include "your.ff/spc.itp"
[system]
whatever name you like
[molecules]
hetero 1
SOL 10123

Mark


> Many thanks for any suggestions.
> Anna
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>