subject:"\[gmx\-users\] Regarding the charge of the atom in the .rtp file"

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

2017-06-22 Thread Justin Lemkul




On 6/22/17 11:23 AM, Dilip H N wrote:

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 HGPAM20.390  2
   HN2 HGPAM20.390  3
   HC1 HGAAM20.090  4
   HC2 HGAAM20.090  5
   HC3 HGAAM20.090  6
   [ bonds ]
N1C1
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..??



You need to go to the original CHARMM force field files.  These include names 
and (typically) chemical structure drawings.


http://mackerell.umaryland.edu/charmm_ff.shtml#charmm

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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

2017-06-22 Thread 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 HGPAM20.390  2
  HN2 HGPAM20.390  3
  HC1 HGAAM20.090  4
  HC2 HGAAM20.090  5
  HC3 HGAAM20.090  6
  [ bonds ]
   N1C1
   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...





   Sent with Mailtrack


On Thu, Jun 22, 2017 at 4:38 PM, Mark Abraham 
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 
> 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 HGPAM20.390  2
> >   HN2 HGPAM20.390  3
> >   HC1 HGAAM20.090  4
> >   HC2 HGAAM20.090  5
> >   HC3 HGAAM20.090  6
> >   [ bonds ]
> >N1C1
> >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...
> >
> >
> >
> >    Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature=en;
> referral=cy16f01.di...@nitk.edu.in=22
> > >
> >
> > On Wed, Jun 21, 2017 at 4:23 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > On Wed, Jun 21, 2017 at 11:59 AM Dilip H N 
> > > 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 HGPAM20.390  2
> > > >  HN2 HGPAM20.390  3
> > > >  HC1 HGAAM20.090  4
> > > >  HC2 HGAAM20.090  5
> > > >  HC3 HGAAM20.090  6
> > > >   [ bonds ]
> > > >   N1C1
> > > >   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
> > > >
> > > >
> > > >
> > > >    Sent with Mailtrack
> > > > <
> > > > https://mailtrack.io/install?source=signature=en;
> > > referral=cy16f01.di...@nitk.edu.in=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-requ...@gromacs.org.
> > > >
> > > --
> > > 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-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > With Best Regards,
>

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

2017-06-22 Thread 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  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 HGPAM20.390  2
>   HN2 HGPAM20.390  3
>   HC1 HGAAM20.090  4
>   HC2 HGAAM20.090  5
>   HC3 HGAAM20.090  6
>   [ bonds ]
>N1C1
>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...
>
>
>
>    Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
>
> On Wed, Jun 21, 2017 at 4:23 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > On Wed, Jun 21, 2017 at 11:59 AM Dilip H N 
> > 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 HGPAM20.390  2
> > >  HN2 HGPAM20.390  3
> > >  HC1 HGAAM20.090  4
> > >  HC2 HGAAM20.090  5
> > >  HC3 HGAAM20.090  6
> > >   [ bonds ]
> > >   N1C1
> > >   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
> > >
> > >
> > >
> > >    Sent with Mailtrack
> > > <
> > > https://mailtrack.io/install?source=signature=en;
> > referral=cy16f01.di...@nitk.edu.in=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-requ...@gromacs.org.
> > >
> > --
> > 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-requ...@gromacs.org.
> >
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Regarding the charge of the atom in the .rtp file

2017-06-21 Thread Dilip H N

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 HGPAM20.390  2
  HN2 HGPAM20.390  3
  HC1 HGAAM20.090  4
  HC2 HGAAM20.090  5
  HC3 HGAAM20.090  6
  [ bonds ]
   N1C1
   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...



   Sent with Mailtrack


On Wed, Jun 21, 2017 at 4:23 PM, Mark Abraham 
wrote:

> Hi,
>
> On Wed, Jun 21, 2017 at 11:59 AM Dilip H N 
> 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 HGPAM20.390  2
> >  HN2 HGPAM20.390  3
> >  HC1 HGAAM20.090  4
> >  HC2 HGAAM20.090  5
> >  HC3 HGAAM20.090  6
> >   [ bonds ]
> >   N1C1
> >   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
> >
> >
> >
> >    Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature=en;
> referral=cy16f01.di...@nitk.edu.in=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-requ...@gromacs.org.
> >
> --
> 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-requ...@gromacs.org.
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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Re: [gmx-users] Regarding the charge of the atom in the .rtp file

2017-06-21 Thread Mark Abraham

Hi,

On Wed, Jun 21, 2017 at 11:59 AM Dilip H N 
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 HGPAM20.390  2
>  HN2 HGPAM20.390  3
>  HC1 HGAAM20.090  4
>  HC2 HGAAM20.090  5
>  HC3 HGAAM20.090  6
>   [ bonds ]
>   N1C1
>   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
>
>
>
>    Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=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-requ...@gromacs.org.
>
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[gmx-users] Regarding the charge of the atom in the .rtp file

2017-06-21 Thread Dilip H N

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 HGPAM20.390  2
 HN2 HGPAM20.390  3
 HC1 HGAAM20.090  4
 HC2 HGAAM20.090  5
 HC3 HGAAM20.090  6
  [ bonds ]
  N1C1
  N1   HN1
  N1   HN2
  C1   HC1
  C1   HC2
  C1   HC3
 ie how are the charges -0.990, -0.060, 0.390 etc., are assigned...

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..??

Any help/suggestion is most welcome.
Thank you...
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



   Sent with Mailtrack

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

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

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

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

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

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

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