Hi,
I think you're going to have to do some experimentation here. Since
you are having difficulty minimizing some of the structures in your
trajectory you may want to extract some of these "problem" frames and
try to minimize them individually. Play around with different
minimizers and their settings, and try to determine why the minimizer
is having so much difficulty with the structures. You can either go
through sander or write your own NAB program to do this - there are
some good examples given in the Amber manual.
Good luck,
-Dan
On Thu, Sep 18, 2014 at 9:47 AM, Sourav Purohit <sour000.gmail.com> wrote:
> Okay. So is there no other way around this problem??? Kindly share ur
> thoughts on this.
>
>
> On Thu, Sep 18, 2014 at 8:08 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> [image: Boxbe] <https://www.boxbe.com/overview> This message is eligible
>> for Automatic Cleanup! (jason.swails.gmail.com) Add cleanup rule
>> <https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Ftoken%3D0ivBGgGMjLNq9XANQS%252FBcvSwDcvc1IsJwS%252FsO33bQUqqdGxUBvG%252BK%252BgTy4PrLbnZhycN51z4cCYjDJVfIj%252FalNjjkC8In4kLacdBt2rgOSTxr7hv9%252BGkXoowdarhwv9Z0OBSSxklDbWJHD%252FePjJpFw%253D%253D%26key%3Dn%252BMJiJWM8oNN0gUTKNS9khK3vx0s4iFfqcE6PUkUvyk%253D&tc_serial=18635512311&tc_rand=1228989360&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001>
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>>
>> On Thu, 2014-09-18 at 19:54 +0530, Sourav Purohit wrote:
>> > Hi,
>> > Thanks for the reply. Is there some way to do minimization in SANDER
>> using
>> > a trajectory file as an input??
>>
>> Look at the imin=5 option (described in the manual). But if the XMIN
>> minimizer in NAB doesn't work, I highly doubt the one in sander will --
>> it is significantly worse.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
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>>
>>
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--
-------------------------
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 Thu Sep 18 2014 - 09:30:07 PDT
