Thanks for the suggestions.
So is there some way to know which are the frames of the trajectory file
that are causing the problem, or how many frames are being rejected.
Finally I get an output and a number for entropy change but don't know
whether to believe the number or not. Some comments on these please.
On Thu, Sep 18, 2014 at 9:24 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> >
> >> | More info
> >> <
> http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=18635512311&tc_rand=1228989360&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
> >
> >>
> >> 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 - 09:30:04 PDT
