[gmx-users] defining parameters in a separate itp file

[Dallas Warren]

Dave,

What you are looking to achieve might be doable using the the .rpt file
(entry for each molecule), specbond.dat (into which you put the special
bond) then run your coordinate file through pdb2gmx, making the entire
topology which will also now include the intermolecular bond.

On Mon, 28 Oct. 2019, 12:24 pm Dave M, <dave.gromax at gmail.com> wrote:

> Hi All,
>
> I am trying to define a bond between two molecules. Their parameters are
> defined in separate itp files: molA.itp and molB.itp. I know I can
> combine both the itp files but I am just wondering if I can define extra
> bonds/angles joining two molecules in a separate itp file taking care of
> atom numbers. To test it I defined an extra bond joining two atoms (elastic
> bond) from two molecules in a separate bond.itp file but it does not look
> like molecules come close at all.
> Not sure this is a correct way. And, also is there a way I can print the
> bond parameters from tpr file to confirm whether all the bonds and angles
> are read from itp files.
>
> My top file looks like this
>
> #include "mol1.itp"
>
> #include "mol2.itp"
>
> #include "bond.itp"
>
>
> [ system ]
>
> test
>
>
> [ molecules ]
>
> ; name        number
>
> molA 1
>
> molB 1
>
>
> Thanks.
> Dave
> --
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On Mon, 28 Oct. 2019, 12:24 pm Dave M, <dave.gromax at gmail.com> wrote:

> Hi All,
>
> I am trying to define a bond between two molecules. Their parameters are
> defined in separate itp files: molA.itp and molB.itp. I know I can
> combine both the itp files but I am just wondering if I can define extra
> bonds/angles joining two molecules in a separate itp file taking care of
> atom numbers. To test it I defined an extra bond joining two atoms (elastic
> bond) from two molecules in a separate bond.itp file but it does not look
> like molecules come close at all.
> Not sure this is a correct way. And, also is there a way I can print the
> bond parameters from tpr file to confirm whether all the bonds and angles
> are read from itp files.
>
> My top file looks like this
>
> #include "mol1.itp"
>
> #include "mol2.itp"
>
> #include "bond.itp"
>
>
> [ system ]
>
> test
>
>
> [ molecules ]
>
> ; name        number
>
> molA 1
>
> molB 1
>
>
> Thanks.
> Dave
> --
> 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.
>