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

[Dilip H N]

No, its not related to parameterization methodology. it is a different
question...

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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On Thu, Jun 22, 2017 at 4:38 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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...
> >
> >
> >
> >   <https://mailtrack.io/> Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature&lang=en&
> referral=cy16f01.dilip at 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
> > > > <
> > > > https://mailtrack.io/install?source=signature&lang=en&
> > > referral=cy16f01.dilip at nitk.edu.in&idSignature=22
> > > > >
> > > > --
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> >
> > DILIP.H.N
> > Ph.D Student
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student