Re: [AMBER] ptraj-clustering

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 26 Jul 2010 23:14:20 -0400

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)
>> > ----------------------------------------------
>> >
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>> _______________________________________________
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>
>


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Received on Mon Jul 26 2010 - 20:30:05 PDT
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