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

[Mark Abraham]

Hi,

I don't understand what you are asking. How does it relate to
parameterization methodology?

Mark

On Thu, Jun 22, 2017 at 7:20 AM Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> Thank you for reply..
>
> But how can i identify the molecule as methylamine (for example) since in
> the .rtp the molecule type is written as [MAM1]
> [ 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
> Is thr any hint such tht i can identify the molecule type written in .rtp
> file.??
> Or should i manually find it out..??... but in case of Glycine the molecule
> type is [GLY] which is easy to find....
> How can i solve this issue..??
>
> Thank you...
>
>
>
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> <
> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22
> >
>
> On Wed, Jun 21, 2017 at 4:23 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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
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> > > https://mailtrack.io/install?source=signature&lang=en&
> > referral=cy16f01.dilip at nitk.edu.in&idSignature=22
> > > >
> > > --
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> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
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