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: > http://atb.uq.edu.au/molecule.py?molid=22625#panel-md > > 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<http://topol.top>, 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 > 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]. Regards Rahul -- *Regards,* *Rahul * -- 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].
