[gmx-users] GB parameter(s) missing or negative but they aint missing nor negative

Dear all, Im trying to run an md or em using an implicit solvation method using gromacs 4.5.5 but I allways get the same errors. GB parameter(s) missing or negative for atom type 'OS' GB parameter(s) missing or negative for atom type 'H2' GB parameter(s) missing or negative for atom type 'N*

[gmx-users] Dangling bond at terminal end of RNA rosetta model

Hi everybody, Im trying to use GROMACS for MD of a RNA model generated by Rosetta (FARFAR). As a test I try processing a modelledpdb file. When I prepare thetopology files (pdb2gmx -f test.pdb -ff amber99 -ignh ) from pdb I encounter following output : Sorting it all out... Opening force fiel