You can minimise the system in vaccum. If it is not running properly there might be some problem in topology. If it is running proper ...you have to delete water molecule from the surface of the protein...and then minimize.
On Tue 19 Nov, 2019, 9:32 PM Justin Lemkul, <[email protected]> wrote: > > > On 11/19/19 10:30 PM, Iman Katouzian wrote: > > Good day. > > > > I have encountered a problem in my protein-ligand simulation as after the > > energy minimization step, when I run the gmx mdrun -deffnm nvt > > I encounter the error segmentation faiulire core dumped : > > > > step 1: One or more water molecules can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > > > Back Off! I just backed up step1b.pdb to ./#step1b.pdb.8# > > > > Back Off! I just backed up step1c.pdb to ./#step1c.pdb.8# > > Wrote pdb files with previous and current coordinates > > *Segmentation fault (core dumped)* > > > http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > [email protected] | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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 [email protected]. > -- 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 [email protected].
