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

[Dina Mirijanian]

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
>
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> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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