Re: [gmx-users] query regarding a topology file

Hi Jagannath, I don't see why you have to "prepare a ff**bon.itp" to go with your molecule.itp. In case the regular bond type definitions are not sufficient, you can just add the bonds, angles, dihedrals directly in the .itp file. The bond_types, angle_types and dihedral_types are mainly used for

Re: [gmx-users] query regarding a topology file

Thanks for reply. Yes, it uses the force-field file I created. Basically I found out that the dihedral which the program skips is also 0. On Apr 12, 2007, at 8:43 PM, Dallas B. Warren wrote: Can't really help you directly, but it comes to mind when I read that error that may be something is

RE: [gmx-users] query regarding a topology file

Can't really help you directly, but it comes to mind when I read that error that may be something is incorrectly defined or formatted within your files. It is not picking up the actual values, or something like that? Is it using the forcefield files you created? Catch ya, Dr. Dallas Warren Lect

[gmx-users] query regarding a topology file

Hi, I am trying to prepare a gromacs topology file for a non-natural peptide. For that I prepared a molecule.itp file and a corresponding ff***bon.itp file which contains all the bond-type, angle-type and dihedral-type. But, when I try to use grompp for generating the .tpr file, it sho