I receive segmentation faults often when running ptraj. However, I
never use "contacts". I use mainly distance and dihedral.
On 2/21/11, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Thanks for the info, good to know it seems isolated to the 'contacts'
> command.
>
> I'm not all that familiar with 'contacts' but I think that it's
> relatively memory-intensive compared to most other actions. I can't
> reproduce your error with a 1000 frame trajectory of a ~50K atom
> system. It seems your system is much larger - could you provide the
> topology and a restart file so I can try to reproduce the error (also
> let me know about how many frames your traj is)? Thanks.
>
> -Dan
>
> On Mon, Feb 21, 2011 at 4:18 PM, Seibold, Stephen <Seibold79.stmary.edu>
> wrote:
>> Hi Dan
>> Yes. Rdparm reads through correctly, stating the number of sets in the
>> trajectory. RMSD and distances can be also calculated without a problem.
>>
>> Thanks Steve
>>
>>
>> -----Original Message-----
>> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
>> Sent: Monday, February 21, 2011 3:00 PM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] PTRAJ and segmentation faults
>>
>> Hi,
>>
>> Is ptraj able to read through the trajectory at all? Does the segfault
>> occur without the 'contacts' command?
>>
>> -Dan
>>
>> On Mon, Feb 21, 2011 at 3:56 PM, Seibold, Stephen <Seibold79.stmary.edu>
>> wrote:
>>> Hi users
>>> I am having problems with the latest ToolSet version. I tried running
>>> "contacts" in ptraj and keep getting a "segmentation fault". I am sending
>>> you my input file and log file.
>>>
>>> Am I doing something wrong? I also tried using a PDB as input instead of
>>> .mdcrd, but it also gave me the segmentation fault.
>>>
>>> INPUT:
>>>
>>> trajin RNAP_openMD39_42.mdcrd
>>>
>>> center :1-2495 mass origin
>>> image origin center familiar
>>>
>>> contacts first byresidue out contact.txt time 10 distance 5.0 .CD
>>>
>>>
>>> go
>>>
>>>
>>> OUTPUT LOG FILE:
>>>
>>> \-/
>>> -/- PTRAJ: a utility for processing trajectory files
>>> /-\
>>> \-/ Version: "AMBER 11.0 integrated" (4/2010)
>>> -/- Executable is: "ptraj"
>>> /-\ Running on 1 processor(s)
>>> \-/ Residue labels:
>>>
>>> MET GLU ILE LYS ARG PHE GLY ARG ILE ARG
>>> GLU VAL ILE PRO LEU PRO PRO LEU THR GLU
>>> ILE GLN VAL GLU SER TYR ARG ARG ALA LEU
>>> GLN ALA ASP VAL PRO PRO GLU LYS ARG GLU
>>> ASN VAL GLY ILE GLN ALA ALA PHE ARG GLU
>>> THR PHE PRO ILE GLU GLU GLU ASP LYS GLY
>>> LYS GLY GLY LEU VAL LEU ASP PHE LEU GLU
>>> TYR ARG LEU GLY GLU PRO PRO PHE PRO GLN
>>> ............
>>> ............
>>>
>>> WAT WAT WAT WAT WAT WAT WAT
>>>
>>> PRMTOP does not contain %FLAG RADIUS_SET
>>> Setting box to be an exact truncated octahedron, angle is 109.471221
>>>
>>> PTRAJ: Processing input from "STDIN" ...
>>>
>>> PTRAJ: trajin RNAP_openMD39_42.mdcrd
>>> Checking coordinates: RNAP_openMD39_42.mdcrd
>>> ./ptraj: line 1: 5109 Segmentation fault ptraj RNAP_open.prmtop
>>>
>>>
>>>
>>> I applied all the new patches, recompiled (gcc on Red Hat enterprise 5)
>>> and the ToolSet passed all its test. Even with the patches does ptraj
>>> have trouble with large trajectories?? I have since switched over to
>>> "netCDF" hoping this will stop the problem.
>>>
>>> Steve Seibold, Ph.D.
>>> Assistant Professor of Chemistry
>>> University of Saint Mary
>>>
>>> _______________________________________________
>>> 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
>>
>
> _______________________________________________
> 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
Received on Mon Feb 21 2011 - 15:30:04 PST
