Hi,
On Tue, Aug 28, 2012 at 9:33 AM, Sanjib Paul <sanjib88paul.gmail.com> wrote:
> Actually
> I want a starting structure for nmode analysis which would have very small
> root-mean-square gradient. I thought after getting a average structure I
> would minimiza it and then that minimized structure would be starting
> structure.
But once you minimize the averaged structure you'll end up with
something different anyway. Averaged structures can be useful as
references for rmsd etc but not much good as a starting structure. Why
not just take the lowest energy structure from your trajectory and
minimize that, or alternatively minimize all of the structures from
your trajectory using an imin=5 run and take the lowest E structure
from that?
-Dan
>
> Sanjib
>
> On Tue, Aug 28, 2012 at 7:43 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> On Tue, Aug 28, 2012 at 10:05 AM, Sanjib Paul <sanjib88paul.gmail.com
>> >wrote:
>>
>> > Dear Amber Users,
>> > I wanted to generate a average structure
>> form 1
>> > ns trajectory file of my protein using 'average' command of ptraj. My
>> input
>> > file is like following:
>> > trajin protein_prod_1ns.mdcrd
>> > average protein_prod_1ns_avg.pdb pdb
>> >
>>
>> Note, the 'average' command does not do any kind of implicit fitting, so
>> you are including free rotation and translation in your average (which is
>> *NOT* something you probably want to do).
>>
>> To get rid of these contributions, add a "rms" command before 'average'.
>>
>>
>> > When I observe my pdb file of average structure I noticed that some
>> portion
>> > of protein is very unstable and very absurd. Atoms are overlapping and
>> some
>> > unusual bonds are also present. Then, I followed analysis portion of
>> > TUTORIAL B3. Here also structure is like before. Some unusual bonds and
>> > overlapped atoms are present. How can I overcome it? Please help.
>> >
>>
>> 'Warped' and 'strange' structures are expected for an average (to some
>> extent). Consider for instance a freely rotating methyl group such that
>> all hydrogens attached to the CH3 are rotationally degenerate. In this
>> case, each hydrogen atom should have the *same* average coordinates which
>> should lie almost directly on top of the C atom they are all attached to.
>>
>> You should think about what you really want and whether or not an 'average'
>> structure satisfies your needs.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
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>>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Aug 28 2012 - 09:30:03 PDT
