[gmx-users] Segmentation fault (core dumped) during EM

Justin Lemkul jalemkul at vt.edu
Thu Apr 23 13:55:34 CEST 2015

On 4/23/15 7:11 AM, Tushar Ranjan Moharana wrote:
> Dear all,
> I want to simulate lid opening of lipase in presence of triglyceride
> micelle. I made micelle and equilibrate it in GROMACS (em, nvt, npt and md
> ) using CHARM36 force field. Dock triglyceride with lipase and put the
> docked complex close to micelle. I changed the atomtype after docking to
> match with CHARM36 atom type. I solvated the micelle lipase complex and
> added required ions for charge neutrality. Then I proceeds to em there I am
> getting the following error
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+03
>     Number of steps    =         2000
> Segmentation fault (core dumped)ot=         -nan Fmax= 1.31533e+09, atom=
> 963
> I have shared some of my file which may be helpful in trouble shooting by
> dropbox (everyone can asses). the links are as follow
> tepa.itp is parameter file for triglyceride (triEPA)
> https://www.dropbox.com/s/mrcaz7r6cbcujm4/tepa.itp?dl=0
> topol.top is the system topology file
> https://www.dropbox.com/s/m6o1m421hdyjnnt/topol.top?dl=0
> wt_gt_wp_tepa_micell_ion.gro is the structure file (just before em)
> https://www.dropbox.com/s/0bd9fk36t00r76w/wt_gt_wp_tepa_micell_ion.gro?dl=0

The coordinates of your protein are all fragmented.  Open in VMD and you will 
see this clearly.


> mdp file for energy minimization
> https://www.dropbox.com/s/ik4heve2hakz7bc/minim.mdp?dl=0
> calcium.itp and zinc.itp are distance restraint to protect the calcium and
> zinc binding domain of my lipase
> https://www.dropbox.com/s/2ebgezf19sctd8f/calcium.itp?dl=0
> https://www.dropbox.com/s/sh12j3ik5uc3lc6/zinc.itp?dl=0
> Any suggestion is most welcome.
> Thanks for your time and effort.
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
> "A society with free knowledge is better place to live than a society with
> free food."


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


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