Hi Jason,
Thanks for the heads up. I applied the relevant patches and recompiled. I am now encountering a strange problem, which I will try to describe best in my sleep deprived state.
I did the following:
1) Applied the patches
2) Compiled sander for an x86_64 system
3) It compiled fine. I stored the executable sander.MPI separately in my home directory. I had to do this, since I don't have root access on the computer. Note that I now have two versions of sander, one stored in $AMBERHOME and another one in my home directory.
4) I then ran test/trajene. It failed by saying "Error 5 Unable to open mdin".
5) I then copied sander.MPI to the trajene directory and ran the trajene test. Worked perfectly.
6) It seems like sander is now refusing to accept relative paths. The previous version that I have, accepts relative paths without a problem. This one takes the location of the sander.MPI executable as the path to look for the mdin and other files.
I would like sander to accept relative paths, mainly because of my pre-exisiting setup which makes heavy use of relative paths. How can I go about doing this?
Thanks
Ganesh Krishnan
Materials Science & Engineering
North Carolina Institute of Technology
--- On Sat, 4/17/10, Jason Swails <jason.swails.gmail.com> wrote:
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] Trajectory Smoothing
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Saturday, April 17, 2010, 2:45 PM
As a follow-up to Dan's description (which is exactly what it sounds like
you're looking for), remember to apply all bugfixes for amber9 and amber10
(the only two released versions that have this capability). Without
applying bugfix 45 for amber9 or 4 for amber10, this will not function as
described in the manual.
While it is always advisable to apply all bugfixes, this problem has been
reported to the list numerous times, so I thought I'd point it out. Don't
forget to re-compile after applying the bugfixes (and make clean beforehand
so that it does not use an old object file or preprocessed source file
without the applied bugfixes).
Good luck!
Jason
On Sat, Apr 17, 2010 at 4:52 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> You can post-process the trajectory with sander using the imin==5 option
> and
> setting maxcyc to the number of steps you want to minimize for. If you set
> ntwx to a non-zero value the minimized frames will be written to whatever
> file is specified by '-x'.
>
> -Dan
>
> On Sat, Apr 17, 2010 at 12:43 PM, Ganesh Krishnan <hereisganesh.yahoo.com
> >wrote:
>
> > How do I energy minimize each frame? As far as I understand, the minimize
> > option in sander takes a restrt file (one frame) and minimizes that. Do
> you
> > mean that I generate restrt files for each frame, minimize each of those
> and
> > recombine them? Thanks for your help.
> >
> > --- On Thu, 4/15/10, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> > From: Bill Ross <ross.cgl.ucsf.edu>
> > Subject: Re: [AMBER] Trajectory Smoothing
> > To: amber.ambermd.org
> > Date: Thursday, April 15, 2010, 7:47 AM
> >
> > > I find that smoothing all the residues results in
> > > unwanted geometric distortions
> >
> > If you energy minimize each frame of the smoothed trajectory,
> > this should clean it up.
> >
> > > So I am looking at smoothing selected residues.
> >
> > I doubt that is possible with current software.
> >
> > Bill
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Postdoctoral Associate
> SAS - Chemistry & Chemical Biology
> 610 Taylor Road
> Piscataway, NJ 08854
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Apr 18 2010 - 00:00:03 PDT
