Hi,
On Fri, Nov 28, 2014 at 8:37 PM, Soumendranath Bhakat
<bhakatsoumendranath.gmail.com> wrote:
> trajin md1.mdcrd
> autoimage
> strip :WAT,Cl- out prefix stripped
> trajout md1_dry.mdcrd
Two minor points here: 1) If you are going to image and strip, it's
best to do the stripping before the imaging - this will be faster. 2)
In your 'strip' command the keyword for writing out a stripped
topology is 'outprefix' (no spaces).
-Dan
> As per the suggestions of Prof D. Case I think the following should work (I
> will try it asap).
>
> trajin md1_dry.mdcrd
> reference Full_Mini_dry.rst
> rms reference out rms_min.dat .CA
> average av.pdb * pdb nobox
>
> Then
>
> trajin md1_dry.mdcrd
> reference av.pdb
> rms reference out rms_min.dat .CA
> atomicfluct out bfactor.dat :1-198.CA byres bfactor
>
> I think the above mentioned script is fine. Please point out if there is
> any mistake or improvement or easy way that might act well.
>
> Regards;
> SB
>
>
> On Fri, Nov 28, 2014 at 7:22 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
>> On Fri, Nov 28, 2014, Soumendranath Bhakat wrote:
>> >
>> > I wish to calculate B factor but I am getting huge values something like
>> > 40539.6099
>> >
>> > I think I am missing aligning with a reference structure. Below a script
>> > please see if it is fine or there is any mistake
>> >
>> > trajin md1_dry.mdcrd
>> > reference Full_Mini.rst
>> > atomicfluct out bfactor.dat :1-198.CA byres bfactor
>>
>> Above won't work: you need to use the rms command to align the structure to
>> the average structure. See the description of the atomicfluct command in
>> the
>> Reference Manual.
>>
>> >
>> > or this one
>> >
>> > trajin md1_dry.mdcrd
>> > reference Full_Mini.rst
>> > rms reference out rms_min.dat .CA
>> > atomicfluct out bfactor.dat :1-198.CA byres bfactor
>>
>> This is better, but yet better would be to use the average structure as
>> a reference. (It's not clear from your email if you are getting really
>> large B-factors from this second script or not.)
>>
>> ...good luck...dac
>>
>>
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>>
>
>
>
> --
> Thanks & Regards;
> Soumendranath Bhakat
> Researcher
> Molecular Modelling and Drug Design Research Group
> Discipline of Pharmaceutical Sciences
> UKZN, Westville
> Weblink: http://soliman.ukzn.ac.za/Home.aspx
> Past: Department of Pharmaceutical Sciences
> Birla Institute of Technology, Mesra, India
> in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/
> _______________________________________________
> 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 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sun Nov 30 2014 - 11:00:02 PST
