Great! Thanks!!! -Israel ________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Dallas Warren <dallas.war...@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. https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FErrors%23System_has_non-zero_total_charge&data=02%7C01%7Cisraele%40cpp.edu%7C2e9ffeb3f8ad43fb2e1008d6f3ae51a3%7C164ba61e39ec4f5d89ffaa1f00a521b4%7C0%7C0%7C636964327356046756&sdata=HGXGwqEHbNRahSnmfaF8AswV11uD0%2B%2B9wp6tjm%2FQRLg%3D&reserved=0 On Tue, 18 Jun. 2019, 1:17 pm Israel Estrada, <isra...@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-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Paul > Bauer <paul.baue...@gmail.com> > Sent: Thursday, June 13, 2019 8:08:58 AM > To: gmx-us...@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, <isra...@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-boun...@maillist.sys.kth.se < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Bratin > > Kumar Das <177cy500.bra...@nitk.edu.in> > > Sent: Wednesday, June 12, 2019 7:00:55 PM > > To: gmx-us...@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.abra...@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, <isra...@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 > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > > > https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7Cisraele%40cpp.edu%7C2e9ffeb3f8ad43fb2e1008d6f3ae51a3%7C164ba61e39ec4f5d89ffaa1f00a521b4%7C0%7C0%7C636964327356046756&sdata=3dt1BUvOZXCukNozE6KLoymKGuXurRYjdLYmft0Qtgo%3D&reserved=0 > > before > > > > posting! > > > > > > > > * Can't post? 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