AMBER Archive (2007)

Subject: Re: AMBER: restraint command not taken

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Mon Apr 02 2007 - 11:16:16 CDT

Hi,

So, your input looks very strange again ...... First, why do you have
"restraint_wt" and "restraintmask" outside the &cntrl namelist ..???

So, what are you actually trying to do ?? restraint_wt and restraintmask
... will keep some atoms fixed and for that you need ntr=1..... On the
other hand as far as I understood you, you want to apply only NMR-like
restraints ...If you want to do that you dont need any restraint_wt and
restraintmask and ntr should be 0 ..... (by the way the mask syntax is
also wrong .... "@" indicates atom and ":" indicates residue -- please
look at the manual ...)... So I am copletely confused and you should
clearly say what you want to do ....

Then, you specify 2 times in your input LISTOUT and DISANG .....

Actually, I am very puzzled that your job managed to run with this kind
of input ....(as I see it it actually took only first lines of input .....)

If you want to do annealing please take the script at page 207 in the
amber9 manual and try it on your system .... See if it works, and only
after that modify it according to your needs ...
Also, did you actually look at the tutorial as I suggested ???

So, this is my last answer on the issue ... First you should do the
tutorial(s) to get basic knkowledge about amber and how it works. You
should try to learn the basic synthax of the input by reading the
approproiate manual sections. When you are confident that you understand
it enough you should take that script in the amber manual, run it ... It
should work on your system also ... But also, keep in mind that that's
an example script so you might want to modify it after you understand
what its doing ....

Good luck ...
vlad

deepti nayar wrote:

> hi
>
> Thanks for all the prevous guidance but i need to ask something.
>
> I am doing simulations of a dimer. howeever, i want to restrain
> movement of few atoms during simulation.but when i look at the output
> file it seems to me as if the command is not accepted. and so the
> atoms are not restrained.
>
> my input file and output file are attached.
>
>
> please guide me
>
> thanks
> deepti 

-- 
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Dr. Vlad Cojocaru

EML Research gGmbH
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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/

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