Hi, Thanks for the input. I’m just trying to get it to run at this point — I’ll worry about the box later.
Could you please elaborate on “you haven’t mentioned those entries in the right way”? The names of the atoms are correct, it’s listed correctly under [ bondtypes ], and the parameters are exactly as taken from the .itp file shared by the ATB database. What other mistake could I be making? Best, Irem > On Apr 8, 2019, at 12:53 AM, RAHUL SURESH <[email protected]> wrote: > > On Mon, Apr 8, 2019 at 10:09 AM Irem Altan <[email protected]> wrote: > >> Hi all, >> >> I’m trying to add the topology for sucrose manually to the force field, >> using the .itp file provided here: >> https://urldefense.proofpoint.com/v2/url?u=http-3A__atb.uq.edu.au_molecule.py-3Fmolid-3D22625-23panel-2Dmd&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=S7EOHss8_RZKlWBIBOMR1Vs4OXaHjqZJpTXfUtbaKUQ&s=CkJYAWZHHTYNI3wnlNXc9RQG_CIrzjdsHPppXHOI2J8&e= >> >> I created the box with a sucrose molecule and with some waters, and tried >> to create a .tpr for energy minimization. However, this gives me the error >> (and similar ones for all bonds, angles, and dihedrals): >> >> ERROR 1 [file >> topol.top<https://urldefense.proofpoint.com/v2/url?u=http-3A__topol.top&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=S7EOHss8_RZKlWBIBOMR1Vs4OXaHjqZJpTXfUtbaKUQ&s=68yuQVcW74WRMsG1aWudIXVnLZYVSfzkrPYBu79MDeA&e=>, >> line 79]: >> No default Bond types >> > > Which actually means you haven't mentioned those entries in the right way. > > >> >> >> Line 79 refers to the bond between the 1st and the 2nd atom, which are >> types HC and C, respectively. So I added this bond to ffbonded.itp, using >> the info provided in the link to the ATB database above: >> >> HC C 2 0.1090 1.2300e+07 ; sucrose HC-C >> >> However, I still get the same error. What am I missing? >> >> I can suggest an alternative approach if you are simulating only sucrose > molecule in the water box. > > 1. Construct a PDB with only one water molecule. > 2. Use pdb2gmx > 3. Then follow the protein-ligand tutorial > > Hope this work > > Best, >> Irem >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists_GMX-2DUsers-5FList&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=S7EOHss8_RZKlWBIBOMR1Vs4OXaHjqZJpTXfUtbaKUQ&s=cagtQNmW6PF697Nt56_P-Pv-BQIpPJX20SgOM3SreUU&e= >> before >> posting! >> >> * Can't post? Read >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=S7EOHss8_RZKlWBIBOMR1Vs4OXaHjqZJpTXfUtbaKUQ&s=pa_dFSHDr1aCKUOyvr_EVxTXYDvP-AGSsOfkPnDn2-w&e= >> >> * For (un)subscribe requests visit >> https://urldefense.proofpoint.com/v2/url?u=https-3A__maillist.sys.kth.se_mailman_listinfo_gromacs.org-5Fgmx-2Dusers&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=S7EOHss8_RZKlWBIBOMR1Vs4OXaHjqZJpTXfUtbaKUQ&s=bXHWnHMbvosgsXWXBzqLq7iQBaHxpGiUXr8ImaSUlEg&e= >> or >> send a mail to [email protected]. > > > > Regards > Rahul > > > -- > *Regards,* > *Rahul * > -- > Gromacs Users mailing list > > * Please search the archive at > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists_GMX-2DUsers-5FList&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=S7EOHss8_RZKlWBIBOMR1Vs4OXaHjqZJpTXfUtbaKUQ&s=cagtQNmW6PF697Nt56_P-Pv-BQIpPJX20SgOM3SreUU&e= > before posting! > > * Can't post? Read > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=S7EOHss8_RZKlWBIBOMR1Vs4OXaHjqZJpTXfUtbaKUQ&s=pa_dFSHDr1aCKUOyvr_EVxTXYDvP-AGSsOfkPnDn2-w&e= > > * For (un)subscribe requests visit > https://urldefense.proofpoint.com/v2/url?u=https-3A__maillist.sys.kth.se_mailman_listinfo_gromacs.org-5Fgmx-2Dusers&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=S7EOHss8_RZKlWBIBOMR1Vs4OXaHjqZJpTXfUtbaKUQ&s=bXHWnHMbvosgsXWXBzqLq7iQBaHxpGiUXr8ImaSUlEg&e= > or send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * 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 [email protected].
