AMBER Archive (2007)

Subject: Re: AMBER: minimization energy query

From: deepti nayar (deepti.icgeb_at_gmail.com)
Date: Fri Mar 30 2007 - 03:03:24 CST

thank you so much sir for your guidance.I am looking inti it and will
ask you again if i need.

On 3/30/07, Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de> wrote:
> Dear Deepti,
>
> Since you are new to this, why dont you try to look at the amber
> tutorials. I believe they are extremely useful for startingbut also for
> double checking certain procedures that one might forget ...
>
> For you, I recommend tutorial A4 (NMR refinement of a DNA duplex ....).
> It is very clear explained there how NMROPT =1 will attempt reading
> weight changes until it finds a &wt type='END'. Therefore, even if you
> dont specify any particular weight changes in your input, the program
> still wants to find the END of &wt namelist ...
>
> Hope this helps
> vlad
>
>
>
> deepti nayar wrote:
>
> > hi amber users
> >
> > I am minimizing a dipeptide containing phe-dehydrophe. when i dont
> > give nmropt=1 in the min.in file, it runs but whn i add nmropt=1 to my
> > min.in file, it gives the following error in the output file
> >
> > I am not very clear wit all the parameters here. I have to carry out
> > minimization first and then simulation in which few atoms are
> > restrained. In pg 199 of amber9, there is given a script, but i xcant
> > make out the command to run it as i have to do the minimization first.
> > I am attaching my min.in filw which is giving errors.
> >
> > please help me as I am new to this thing. Any sugguestions are welcome
> >
> > thanks
> > deepti
> >
> > Begin reading energy term weight changes/NMR restraints
> > WEIGHT CHANGES:
> > ERROR: No "wt" namelist with TYPE=END found
> >
> > On 3/29/07, deepti nayar <deepti.icgeb_at_gmail.com> wrote:
> >
> >> thank you for replying Dr.Cojocaru
> >>
> >> I will send you the complete details soon.
> >>
> >> On 3/29/07, Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de> wrote:
> >> > Dear Nayar,
> >> >
> >> > I am afraid nobody will be able to answer your question because your
> >> > message doesnt contain any details. For instance you could provide
> >> the 2
> >> > inputs, samples of the 2 outputs so that people may understand what is
> >> > actually going on.
> >> >
> >> > Reading and answering your last email, my guess is that you made
> >> another
> >> > input mistake, but I cannot say anything till you provide us with more
> >> > specific info about your runs ..
> >> >
> >> > cheers
> >> > vlad
> >> >
> >> >
> >> > deepti nayar wrote:
> >> >
> >> > > I hav run energy minimization of a dipeptide in 2 ways
> >> > >
> >> > > In the first attempt, i have run minimization of the complete
> >> > > structure and in the 2nd attempt I have fixed a few atoms and
> >> then run
> >> > > minimization. As far as i think, i should get some difference in the
> >> > > energies of the two runs but what i am getting is exactly the same.
> >> > >
> >> > > please guide me.
> >> > >
> >> > > thanks
> >> > > deepti
> >> > >
> >> -----------------------------------------------------------------------
> >> > > The AMBER Mail Reflector
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> >> > >
> >> >
> >> > --
> >> >
> >>
> ----------------------------------------------------------------------------
> >>
> >> > Dr. Vlad Cojocaru
> >> >
> >> > EML Research gGmbH
> >> > Schloss-Wolfsbrunnenweg 33
> >> > 69118 Heidelberg
> >> >
> >> > Tel: ++49-6221-533266
> >> > Fax: ++49-6221-533298
> >> >
> >> > e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
> >> >
> >> > http://projects.villa-bosch.de/mcm/people/cojocaru/
> >> >
> >> >
> >>
> ----------------------------------------------------------------------------
> >>
> >> > EML Research gGmbH
> >> > Amtgericht Mannheim / HRB 337446
> >> > Managing Partner: Dr. h.c. Klaus Tschira
> >> > Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
> >> > http://www.eml-r.org
> >> >
> >>
> ----------------------------------------------------------------------------
> >>
> >> >
> >> >
> >> >
> >> -----------------------------------------------------------------------
> >> > The AMBER Mail Reflector
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> >> >
> >>
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>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
>
> Tel: ++49-6221-533266
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
> ----------------------------------------------------------------------------
> EML Research gGmbH
> Amtgericht Mannheim / HRB 337446
> Managing Partner: Dr. h.c. Klaus Tschira
> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
> http://www.eml-r.org
> ----------------------------------------------------------------------------
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
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