[gmx-users] Grompp not producing tpr files

Israel Estrada israele at cpp.edu
Tue Jun 18 15:21:55 CEST 2019


Great! Thanks!!!
-Israel

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Dallas Warren <dallas.warren at monash.edu>
Sent: Monday, June 17, 2019 10:31:43 PM
To: GROMACS users
Subject: Re: [gmx-users] Grompp not producing tpr files

Before you go any further you need to correct the topology. The complete
molecule should only have an integer charge, and if it does have a charge
then neutralise the system with counter ions.

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On Tue, 18 Jun. 2019, 1:17 pm Israel Estrada, <israele at cpp.edu> wrote:

> Thanks again for the replies,
>
>
> I'm currently using gromacs 2019.3, and I'm creating a simple system with
> only a monomer in water. The monomer's topology was created using TPP, for
> use with the OPLS force field.
>
>
> After adding the new residue to the force field, I'm able to run
> "pdb2gmx", "editconf", and "solvate" with no issues to create the system.
> It's when I try to "grompp" that the segmentation fault occurs.
>
>
> The only thing that stands out is the system's charge. After running
> pdb2gmx, the system's overall charge is listed as -1.589 e.
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Paul
> Bauer <paul.bauer.q at gmail.com>
> Sent: Thursday, June 13, 2019 8:08:58 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Grompp not producing tpr files
>
> Hello,
>
> Yes, the last part indicates an error that should not happen.
>
> Which version did you use to run this?
>
> If it is a version before 2018, can you try the newer versions to see if
> the error persists?
>
> Cheers
>
> Paul
>
>
>
> On Thu, 13 Jun 2019, 17:04 Israel Estrada, <israele at cpp.edu> wrote:
>
> > Thanks for the replies!
> >
> > Mark, the process seemed to "finish" properly (my terminal did not close,
> > and the command line was waiting for the next command as if it ran
> > normally). I looked for the output file (ions.tpr) in the working
> > directory, or any new files, but nothing was generated.
> >
> > Bratin, here is what my terminal displayed,
> > "command line:
> > gmx grompp -f ions.mdp -c box.gro -o ions.tpr -p topol.top
> >
> > Setting the LD random seed to 973096069
> > Segmentation fault (core dumped)"
> > The last part seems to be the error, right?
> >
> > Thanks again!!
> > -Israel
> >
> > ________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Bratin
> > Kumar Das <177cy500.bratin at nitk.edu.in>
> > Sent: Wednesday, June 12, 2019 7:00:55 PM
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Grompp not producing tpr files
> >
> > Hi
> >    Give here the full error
> >
> > On Thu 13 Jun, 2019, 1:35 AM Mark Abraham, <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > Was grompp exiting normally, or crashing? Are you looking in the right
> > > place, for a file of the right name? :-)
> > >
> > > Mark
> > >
> > > On Wed., 12 Jun. 2019, 18:42 Israel Estrada, <israele at cpp.edu> wrote:
> > >
> > > > Hello users,
> > > >
> > > >
> > > > I'm running into problems trying to grompp; I'm using the command
> > > >
> > > >
> > > > gmx grompp -f ions.mdp -c etc_box.gro  -o ions.tpr -p topol.top
> > > >
> > > >
> > > > and the process shows no error messages, but output files are not
> being
> > > > generated. I'm running this on a small molecule, about 20 atoms, with
> > the
> > > > hopes that I can modify OPLS parameters as needed. I'm sure the
> problem
> > > is
> > > > related to an error in the topology files, but I don't know how or
> if I
> > > can
> > > > fix this.
> > > >
> > > >
> > > > Any help would be greatly appreciated, thank you!
> > > >
> > > > -Israel
> > > > --
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