Re: [gmx-users] generating a top file

Shahrokh Safarian wrote: Dear colleagues As you know if we want to introduce a new molecule into Gromacs, the related parameters for that molecule (e.g. [atoms], [bonds], [pairs], [dihedrals] and so on) should be inserted to the Gromacs rtp file. Strictly, no. Only if you want pdb2gmx to recog

Re: [gmx-users] generating a top file

This is called parameterization. http://wiki.gromacs.org/index.php/Parameterization For small molecule, you can opt for PRODRG for GROMOS/GROMACS force fields; or Antechamber for AMBER force field. Once you obtained the topology, convert them back to the format in the rtp file according to the

[gmx-users] generating a top file

Dear colleagues As you know if we want to introduce a new molecule into Gromacs, the related parameters for that molecule (e.g. [atoms], [bonds], [pairs], [dihedrals] and so on) should be inserted to the Gromacs rtp file. In the Gromacs user's manual (page 100) an example for these types of topolo