Once you define the [ bondedtypes ] in the rtp file like this. 1 1 3 1 1 3 1 0 here the dihedral type function is 3 that means all the dihedrals you define in the aminoacids.rtp file will be taken as type 3. Even I had the the same problem, I was using function type 3 and 5, pdb2gmx takes function 5 as 3. Not a problem you can write a script or do it manually to replace the number 5 to 3.
On Thu, Aug 6, 2015 at 8:26 AM, Zhenhai Li <[email protected]> wrote: > Dear GMX-users, > > Recently I am trying to adding a residue to a force field. I have followed > the instruction of "how to adding residue" on the website. And right now I > can generate the top file from PDB file with pdb2gmx command. However some > of the angle function in the residue is different from the default one in > rtp file in the force field. Therefore there are some mistake on the angle > function of the new residue in the top file generated by pdb2gmx. And when > I use grompp command to generate .tpr file, I will get error like "No > default U-B types" > > I am not sure if there's a way to define angle type for specific angle > interaction in force field to make pdb2gmx overwrite angle function type > for those angle interaction, or I have to manually change those angle type? > > Thank you very much > > -- > Zhenhai > -- > 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]. > -- 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].
