[gmx-users] Grompp not producing tpr files
Israel Estrada
israele at cpp.edu
Tue Jun 18 05:17:04 CEST 2019
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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