For the sake of record, I'm forwarding this to the mailing list as
well. Are you able to pass all tests after installation?
All the best,
Ray
---------- Forwarded message ----------
From: Qin Cai <qcai.uci.edu>
Date: Wed, Nov 30, 2011 at 3:25 PM
Subject: Re: [AMBER] error by running MMPBSa
To: "Ray Luo, Ph.D." <ray.luo.uci.edu>
Cc: urszula.uchiechowska.chem.umu.se
I was able to run pbsa with these options.
I'm using AT1.5 with all latest bug fixes.
Best,
Qin
On Nov 30, 2011, at 9:42 AM, Ray Luo, Ph.D. wrote:
> Okay, I'm asking Qin to take a look of your system and setup ...
>
> All the best,
> Ray
>
>
> ---------- Forwarded message ----------
> From: Urszula Uciechowska <urszula.uchiechowska.chem.umu.se>
> Date: Wed, Nov 30, 2011 at 6:12 AM
> Subject: Re: [AMBER] error by running MMPBSa
> To: AMBER Mailing List <amber.ambermd.org>
>
>
>
> I attached my mmpbsa input file, topology and one snapshot on which i
> am trying to check the mmpbsa. My system is quite small, contains
> 170atoms (peptide). Could you have a look at it and check if its
> working with you?
>
> thank you in advance
> /Urszula
>
>
>
> ________________________________________
> Von: Jason Swails [jason.swails.gmail.com]
> Gesendet: Mittwoch, 30. November 2011 14:58
> An: AMBER Mailing List
> Betreff: Re: [AMBER] error by running MMPBSa
>
> A segfault out of context contains No useful information. You'll need
> to send more details, or if there are none, details about your system,
> options, and what may be unusual about your system. You may even have
> to send your files so we can debug it directly.
>
> One thing to look at is if you have enough memory. Do you know how
> much your job uses compared to how much you have available?
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Nov 30, 2011, at 8:16 AM, Urszula Uciechowska
> <urszula.uchiechowska.chem.umu.se> wrote:
>
>> Dear Amber users,
>>
>> I am trying to run mmpbsa, however I am getting errors:
>>
>> p
>> forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> Image PC Routine Line Source
>> pbsa 000000000041AC11 Unknown Unknown Unknown
>> pbsa 000000000040F10A Unknown Unknown Unknown
>> pbsa 0000000000406810 Unknown Unknown Unknown
>> pbsa 0000000000404F1C Unknown Unknown Unknown
>> pbsa 0000000000401D9C Unknown Unknown Unknown
>> libc.so.6 000000310641D994 Unknown Unknown Unknown
>> pbsa 0000000000401CA9 Unknown Unknown Unknown
>>
>>
>> what is the problem here?
>>
>> /Urszula
>> _______________________________________________
>> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> <mm_pbsa_binding.in><REC.prmtop><snapshot_rec.crd.1>
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Received on Wed Nov 30 2011 - 16:00:04 PST
