Hi, Daniel,
Thank you for debugging and providing the patches.
Jianyin Shao
On Mon, Jul 26, 2010 at 9:14 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Turns out there were a few bugs in the clustering code. The attached
> patch should fix the issue you've been having. Instructions for
> applying the patch are located at the head of the file. Briefly, cd to
> your AMBERHOME directory and apply the patch:
>
> patch -p0 -N < patch_file
>
> Then recompile. Let me know if you still have issues after that. Good luck.
>
> -Dan
>
> On Mon, Jul 26, 2010 at 2:43 AM, Necmettin Pirinccioglu
> <pirincn.dicle.edu.tr> wrote:
> > Dear Danial,
> > Thank you very much for your kind reply. Here I send attached the files
> you request. The
> > compiler is ifort and the version of amber is 9.
> > best wishes,
> > necmettin
> >
> > ---------------------------------------
> > Necmettin Pirinccioglu
> > Department of Chemistry
> > University of Dicle
> > e-mail. pirincn at dicle dot edu dot tr
> > phone. +90 (0412) 2488550 (ext. 3055)
> > ----------------------------------------------
> >
> >
> >> -----Original Message-----
> >> From: Daniel Roe <daniel.r.roe.gmail.com>
> >> To: AMBER Mailing List <amber.ambermd.org>
> >> Date: 23-07-2010 17:36
> >> Subject: Re: [AMBER] ptraj-clustering
> >>
> >> On Fri, Jul 23, 2010 at 3:28 AM, Necmettin Pirinccioglu
> >> <pirincn.dicle.edu.tr> wrote:
> >> >
> >> > cluster out clusters crown all amber representative pdb average pdb
> averagelinkage
> > sieve
> >> > 10 clusters 10 rms :1-1
> >>
> >> Are you sure this is the command you are using? As it is written it
> >> would generate a syntax error in ptraj since 'crown' is not a keyword
> >> the cluster action recognizes.
> >>
> >> I tested the cluster command in ptraj (without 'crown', but otherwise
> >> the same as written above) on 100 frames of a 268 residue system and
> >> it was able to complete without segfaulting (AT1.4 running on linux
> >> x86_64, gnu 4.4.3 compilers).
> >>
> >> In order to troubleshoot this, can you let me know the compiler
> >> type/version used to compile, the version of AmberTools you have, the
> >> architecture and OS/version you are running on, and can you send your
> >> full ptraj output as an attached text file? Thanks.
> >>
> >> -Dan
> >>
> >> > ---------------------------------------
> >> > Necmettin Pirinccioglu
> >> > Department of Chemistry
> >> > University of Dicle
> >> > e-mail. pirincn at dicle dot edu dot tr
> >> > phone. +90 (0412) 2488550 (ext. 3055)
> >> > ----------------------------------------------
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > _______________________________________________
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> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >> _______________________________________________
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> >
> >
>
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Received on Tue Jul 27 2010 - 13:00:03 PDT
