AMBER Archive (2004)

Subject: Re: AMBER: Sander & fix atoms

From: Viktor Hornak (hornak_at_csb.sunysb.edu)
Date: Thu Jun 03 2004 - 16:14:10 CDT


This (your input file) won't work (it mixes amber8 features with amber7)
and I think it is unnecessary to minimize structure in so many steps.
Unless there is something seriously wrong with your initial structure
the minimization won't change it much. I would just simply minimize your
structure with no restraints (delete all group inputs from your input
file) and you may compare your minimized and initial structure to see
how much they differ.

Cheers,
-Viktor

bybaker_at_itsa.ucsf.edu wrote:

>Hello, Viktor:
>
>Thanks for the help.
>
>I use Amber7 for running sander. The idea is to run energy minimization
>on a protein model. The minimization will be done in three steps: (1)
>fixed heavy atoms (all but hydrogen), (2) fixed backbone atoms with
>tethered atoms, (3) tethered backbone atoms. The structure will be then
>subjected to final run with no atom fixed. I am not familiar with
>positional restrains. The purpose is to minimize the whole system rather
>than the specific fragments.
>
>The follow is my input file. Please fell free to give your comments.
>
>Thank you.
>
>Regards
>
>Bo Yang
>
>------ Start-----
>Initial minimization test 1
> &cntrl
> imin=1,
> maxcyc=500,
> ncyc=250,
> ntb=0,
> ntr=0,
> &end
> Group input for restrained heavy atoms (all but hydrogen)
> ATOM ! @H=
> END
> Group input for restrained backbone atoms with tethered atoms
> ATOM @CA, C, O, N
> END
> Group input for tethered backbone atoms
> ATOM @O, H
> END
> END
>
>----- End----
>
>
>On Thu, 03 Jun 2004 13:22:55 -0400 Viktor Hornak wrote:
>
>
>>bybaker_at_itsa.ucsf.edu wrote:
>>
>>
>>>Hello, Amber:
>>>
>>>I would like to run energy minimization in sander with some
>>>
>>restrictions.
>>
>>I'd suggest to use positional restraints (rather than fixing atoms =
>>ibelly flag) - check ntr flag in amber manual. You don't say which
>>version of amber you are using. Depending on that your input file might
>>look differently.
>>In amber8, you'd specify 'restraint_wt' and 'restraintmask' in your
>>&cntrl input section. This could translate to the following for what you
>>want (if I understood your description of restrictions well):
>>
>>
>>>How can I set the minimization inputs with following restrictions:
>>>
>>>--- fix heavy (all but hydrogens) atoms
>>>
>>>
>>restraintmask='!@H='
>>
>>
>>>--- fix backbone atoms
>>>
>>>
>>restraintmask='@CA,C,O,N,H'
>>
>>
>>>--- fix backbone atoms with tethered heavy atoms
>>>
>>>
>>restraintmask='@CA,C,O,N' (?? - maybe that's not what you want but you
>>get an idea)
>>
>>
>>>--- tethered backbone atoms
>>>
>>>
>>restraintmask='@O,H' (??)
>>
>>Check chapter 11.5 in amber8 manual for more detailed description of
>>selection syntax.
>>
>>If you are using amber7 or previous, carefully read "GROUP
>>specification" appendix in amber manual.
>>
>>Hope this helps...
>>
>>-Viktor
>>
>>
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>
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