On Fri, Aug 20, 2021 at 3:26 PM Satyen Dhamankar <[email protected]> wrote: > > I see that VOTCA is running the following command: > gmx_196 grompp -n index.ndx -f grompp.mdp -p topol.top -o topol.tpr -c > conf.gro > > And I am getting the following error: > Molecule type PNM contains no atoms > > This is my topol.top file: > > [ defaults ] > > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > > 1 1 no 0.0 0.0 > > [ atomtypes ] > > ; type mass charge ptype sigma epsilon > > TB 29.04 0.000 A 0.0000 1.0000 > > TA 43.00 0.000 A 0.0000 1.0000 > > TI 43.00 0.000 A 0.0000 1.0000 > > TW 18.01 0.000 A 0.0000 1.0000 > > [ moleculetypes ] More a question for the gromacs mailing list, but I believe this needs two [ moleculetype ] sections instead, see https://github.com/votca/csg-tutorials/blob/master/urea-water/ibi/topol.top#L11-L23
Christoph > > ; Name nrexcel > > PNM 3 > > WT 1 > > [ atoms ] > > ; nr type resnr residue atom cgnr charge mass typeB > chargeB massB > > 1 TB 1 PNM BB 1 0 29.04 > > 2 TA 1 PNM BA 1 0 43.00 > > 3 TI 1 PNM BI 1 0 43.00 > > 4 TW 1 WT BW 1 0 18.01 > > [ bonds ] > > ;ai aj funct c0 c1 c2 c3 > > 1 2 8 1 1.0 > > 2 3 8 1 1.0 > > [ angles ] > > ;ai aj ak funct c0 c1 c2 > > 1 2 3 8 1 1.0 > > [ molecules ] > > ; > > PNM 1 > > WT 4046 > > I don’t understand what is causing this error. I have written similar types > of topol.top files, and it seems to be working just fine. > > For completeness sake, this is my conf.gro file: > > > what a nice title > > 4049 > > 1PNM BB 1 2.229 1.514 4.238 > > 1PNM BA 2 2.272 1.286 4.235 > > 1PNM BI 3 2.194 1.048 4.125 > > 2WT BW 4 2.276 1.580 1.676 > > 3WT BW 5 0.119 0.703 0.277 > > 4WT BW 6 1.682 0.128 4.229 > > 5WT BW 7 4.889 2.252 2.343 > > . > > . > > . > > 4045WT BW 4047 1.332 2.041 1.148 > > 4046WT BW 4048 0.125 1.348 4.089 > > 4047WT BW 4049 0.839 1.673 3.898 > > 4.98674 4.98674 4.98674 0.00000 0.00000 0.00000 0.00000 > 0.00000 0.00000 > > I would appreciate any advice you have for me! > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/e6cc499c-35e8-454d-bd08-23c28861cd01n%40googlegroups.com. -- Christoph Junghans Web: http://www.compphys.de -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e7vmpMkNFsn77-isFt3kfJ4fCxEQEfxe6P%3DGgyFRvvWxw%40mail.gmail.com.
