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 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." -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
