Dear Amber users,
Which formula was used to calculate "divergence" ?
How this command differs from 'kldiv' command as given in Amber manual 14
(section 28.12.10) and also as used in the previous post "
http://archive.ambermd.org/201508/0109.html" ?
Thank you,
Mahendra Thapa
On Mon, Apr 21, 2014 at 10:24 AM, Thapa, Mahendra (thapamb) <
thapamb.mail.uc.edu> wrote:
>
>
>
> ________________________________________
> From: Daniel Roe
> Sent: Monday, April 21, 2014 8:24:06 AM (UTC-06:00) Central America
> To: AMBER Mailing List
> Subject: Re: [AMBER] FW: How to use "divergence" command
>
> Hi,
>
> On Mon, Apr 21, 2014 at 8:15 AM, Mahendra B Thapa <thapamb.mail.uc.edu>
> wrote:
> > cpptraj
> >> divergence ds1 phi_sample1.dat ds2 phi_sample2.dat
> >
> > *What error message I got:*
> > Error: Data set ds1 not found.
> > Error: Could not setup analysis [divergence]
>
> Did you read in the data previously with the 'readdata' command? If
> not, you need to add those commands prior to 'divergence', e.g.,
>
> readdata phi_sample1.dat
> readdata phi_sample2.dat
> divergence ds1 phi_sample1.dat ds2 phi_sample2.dat
>
> Hope this helps,
>
> -Dan
>
> >
> > Hope, these might be helpful in clearing the issue.
> > Thank you for help,
> > Mahendra Thapa
> >
> >
> >
> > On Fri, Apr 18, 2014 at 4:09 PM, Thapa, Mahendra (thapamb) <
> > thapamb.mail.uc.edu> wrote:
> >
> >>
> >>
> >>
> >> ________________________________________
> >> From: Daniel Roe
> >> Sent: Friday, April 18, 2014 2:05:56 PM (UTC-06:00) Central America
> >> To: AMBER Mailing List
> >> Subject: Re: [AMBER] How to use "divergence" command
> >>
> >> Hi,
> >>
> >> You need to post at least your entire cpptraj input (and ideally the
> >> output), as well as the version of cpptraj you are trying to use
> >> before we can help. I suspect there may be some warnings prior to the
> >> error message which may be useful in diagnosing your problem.
> >>
> >> -Dan
> >>
> >> On Fri, Apr 18, 2014 at 10:53 AM, Mahendra B Thapa <thapamb.mail.uc.edu
> >
> >> wrote:
> >> > Dear Amber users
> >> >
> >> > I tried to use the command "divergence" as given in ambertool14:
> >> > divergence ds1 <ds1> ds2 <ds2>
> >> >
> >> > But, I am getting the message as:
> >> > Error: Could not setup analysis [divergence]
> >> >
> >> > Please help me in this issue. I did a couple of trials with different
> >> data
> >> > sets, but no luck.
> >> >
> >> > Thank you for help
> >> > Mahendra Thapa
> >> > University of Cincinnati,OH
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 201
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Dec 09 2015 - 05:30:02 PST
