[gmx-users] Regarding the charge of the atom in the .rtp file

[Mark Abraham]

Hi,

On Wed, Jun 21, 2017 at 11:59 AM Dilip H N <cy16f01.dilip at nitk.edu.in>
wrote:

> Hello all.
> 1] I want to knw how the charges are designated/assigned for the each atoms
> in molecule in the .rtp file.  ie., as example for methylamine in CHARMM
> FF:-
>
> [ MAM1 ]
>   [ atoms ]
>   N1 NG321        -0.990  0
>   C1 CG3AM2     -0.060  1
>  HN1 HGPAM2    0.390  2
>  HN2 HGPAM2    0.390  3
>  HC1 HGAAM2    0.090  4
>  HC2 HGAAM2    0.090  5
>  HC3 HGAAM2    0.090  6
>   [ bonds ]
>   N1    C1
>   N1   HN1
>   N1   HN2
>   C1   HC1
>   C1   HC2
>   C1   HC3
>  ie how are the charges -0.990, -0.060, 0.390 etc., are assigned...
>

The parameterization methodology is unique to each force field, and perhaps
to each tool that generates compatible topologies. You need to read that
documentation and literature to understand how they were derived.


> 2] and if i get the topology/itp file from the automated topology builder
> as in SwissParam for CHARMM forcefield, how can i confirm that the charges
> assigned are exact..??
>

You can see if they are correct in the sense of being a valid model of
reality by running a simulation and observing whether you can get
reasonable agreement with suitable e.g. experimental data.

Mark


> Any help/suggestion is most welcome.
> Thank you...
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>   <https://mailtrack.io/> Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22
> >
> --
> 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.
>