[gmx-users] minimization is not converging
Bratin Kumar Das
177cy500.bratin at nitk.edu.in
Thu Sep 6 15:52:18 CEST 2018
Respected Dr Justin,
I took one membrane protein pdb file
and converted it to .gro using pdb2gmx. Next I builded and packed the POPC
phospholipids bylayer using vmd membrane builder plugin. Subsequently I
solvated the system in vmd only. The entire system was converted to .gro
and all the water molecules and POPC molecules making bad contacts are
deleted. I added ions to nutralize the system in gromacs using genion.
Prior to that all the POPC topoloy properly included in topol.top. prior to
energy minimization all the steps ran with out fatal error. I followed the
procidure explained in gromacs tutorial. Evrey cases the same error is
coming during minimization.
On Thu, Sep 6, 2018, 7:06 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> On 9/6/18 9:34 AM, Bratin Kumar Das wrote:
> > Respected Dr Justin,
> > In pdb2gmx command i used -ignh
> > to ignore the hydrogens. Previously with out using this flag gave missing
> > atom error. May be some hydrogens were missed. Is it possible that the
> > error happening due to the flag (ignh).
> No, because that's not what -ignh does.
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * 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-request at gromacs.org.
More information about the gromacs.org_gmx-users