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

[Justin Lemkul]

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

==================================================