[gmx-users] g_chi Segmentation fault for -maxchi greater than 3

[Dina Mirijanian]

OK. WIll do.  For FYI here are the versions I tested and the version that
worked:
GROMACS/5.0.6        NO
GROMACS/5.0.5        NO
GROMACS/5.0.4        NO
GROMACS/4.6.3        NO
GROMACS/4.5.5        YES!

On Fri, Aug 28, 2015 at 11:33 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/28/15 11:30 AM, Dina Mirijanian wrote:
>
>> I found that with an older version g_chi works fine for the system.
>> Thanks
>> for your help.
>>
>>
> Then we clearly have a bug that needs to be fixed.  If you would, please
> upload a test case (.tpr and a single coordinate file should do it) to
> redmine.gromacs.org with your command line and/or link to this thread.
>
> -Justin
>
>
>
>> On Thu, Aug 27, 2015 at 9:15 PM, Dina Mirijanian <dmirij at brandeis.edu>
>> wrote:
>>
>> No. I have ARG and LYS residues. And I checked the protein trajectory
>>> after trjconv and these residues seemed to be whole.
>>>
>>>
>>> On Thursday, August 27, 2015, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 8/27/15 12:33 PM, Dina Mirijanian wrote:
>>>>
>>>> Hello,
>>>>>
>>>>> I have done a simulation of two protein segments in water and ions.  I
>>>>> have
>>>>> processed my trajectory from the simulation with trjconv using the flag
>>>>> "-pbc whole" in order to make all the bonds whole again, lets call the
>>>>> output trajectory from this "prot_whole.xtc".
>>>>>
>>>>> I then run "g_chi -s protein_whole.pdb  -f prot_whole.xtc -all -maxchi
>>>>> 6"
>>>>> to get the files with all the dihedrals.  I get the following writeout
>>>>> before it crashes:
>>>>> 257 residues with dihedrals found
>>>>> 1184 dihedrals found
>>>>> Reading frame   13000 time 325000.000
>>>>> Segmentation fault (core dumped)
>>>>>
>>>>> However when I run the same g_chi command line with -maxchi 1 it runs
>>>>> fine
>>>>> and writes out the .xvg files with the dihedrals:
>>>>> 257 residues with dihedrals found
>>>>> 1184 dihedrals found
>>>>> Reading frame   13000 time 325000.000
>>>>> j after resetting (nr. active dihedrals) = 983
>>>>> Printing chi1VAL20.xvg
>>>>>
>>>>> The g_chi command works fine for -maxchi 1,2,3  but gives a
>>>>> Segmentation
>>>>> fault for -maxchi 4,5,6.
>>>>>
>>>>> I'm having a hard time figuring out what the problem is.  Has anyone
>>>>> ever
>>>>> run into this problem?
>>>>> I am using gromacs 5.0.5
>>>>>
>>>>>
>>>>> Probably your structure doesn't have any residues with >3 chi torsions.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 629
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>> ==================================================
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>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
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