AMBER Archive (2007)

Subject: Re: AMBER: minimization energy query

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri Mar 30 2007 - 02:28:03 CST

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
>> > > To post, send mail to amber_at_scripps.edu
>> > > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>> > >
>> >
>> > --
>> >
>> ----------------------------------------------------------------------------
>>
>> > 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
>> > To post, send mail to amber_at_scripps.edu
>> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>> >
>>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> 

-- 
----------------------------------------------------------------------------
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
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu