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

[Dina Mirijanian]

I found that with an older version g_chi works fine for the system.  Thanks
for your help.


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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>