Thank you very much !
***************
Kind regards
*Md Fulbabu Sk*
*Ph.D. Research ScholarDiscipline of BioSciences and Biomedical Engineering
(BSBE)Indian Institute of Technology Indore (IITI), India*
Computational BioPhysics Group IITI (Kar's Lab)
<
https://iitibsbeparimalkar.wixsite.com/biophysics>
On Thu, Jan 3, 2019 at 6:58 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> As stated in the manual, the output from the vector command is ’Vx Vy
> Vz Ox Oy Oz’ where V denotes vector coordinates and ’O’ denotes origin
> coordinates. If you want magnitude as well specify the 'magnitude'
> keyword - see the manual for full details.
>
> -Dan
>
> On Wed, Jan 2, 2019 at 11:39 PM Fulbabu Sk <phd1701171005.iiti.ac.in>
> wrote:
> >
> > Dear all,
> > In the output data file, there are 7 columns, but I don't identify which
> > one is dipole moment column.
> > Please clarify the 7 columns.
> >
> >
> >
> >
> >
> > ***************
> > Kind regards
> >
> > *Md Fulbabu Sk*
> >
> >
> >
> > *Ph.D. Research ScholarDiscipline of BioSciences and Biomedical
> Engineering
> > (BSBE)Indian Institute of Technology Indore (IITI), India*
> > Computational BioPhysics Group IITI (Kar's Lab)
> > <https://iitibsbeparimalkar.wixsite.com/biophysics>
> >
> >
> > On Thu, Jan 3, 2019 at 7:16 AM Xiaocong Wang <wangxiaocong.outlook.com>
> > wrote:
> >
> > > Thank you very much!
> > >
> > > Dividing by 0.2082 is correct.
> > >
> > > Best regards,
> > >
> > > Xiao
> > >
> > >
> > >
> > > ________________________________
> > > From: Daniel Roe <daniel.r.roe.gmail.com>
> > > Sent: Thursday, January 3, 2019 2:52:13 AM
> > > To: AMBER Mailing List
> > > Subject: Re: [AMBER] Calculated dipole moment in AMBER
> > >
> > > Hi,
> > >
> > > > I read one post, which says the unit for dipole moment calculated
> from
> > > AMBER cpptraj is not Debye(D). And, the code for calculating dipole
> moment
> > > may be out-dated.
> > >
> > > CPPTRAJ (like the rest of Amber) uses the AKMA unit system, so charge
> > > is in electrons and length is in Angstroms, meaning the dipole is in
> > > units of e * Ang; you'll have to convert to get to Debye (I believe
> > > the conversion is dividing by ~ 0.2082 but you should double check).
> > >
> > > The output format of 'dipole' command is outdated - the 'vector
> > > dipole' code is fine.
> > >
> > > -Dan
> > >
> > > On Wed, Jan 2, 2019 at 10:22 AM Xiaocong Wang <
> wangxiaocong.outlook.com>
> > > wrote:
> > > >
> > > > Dear all,
> > > > I used cpptraj to calculate the dipole moment for a sugar. But, the
> > > value is very different from that calculated in QM.
> > > > Codes are as follows:
> > > >
> > > > trajin sugar.rst7
> > > > vector v1 :1-2 dipole out sugar_dipole.txt
> > > > go
> > > >
> > > > I read one post, which says the unit for dipole moment calculated
> from
> > > AMBER cpptraj is not Debye(D). And, the code for calculating dipole
> moment
> > > may be out-dated.
> > > > Can I get some help on this issue?
> > > > Thank you very much!
> > > > Best,
> > > > Xiao
> > > >
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Received on Thu Jan 03 2019 - 19:30:02 PST
