> saveAmberParmPert solvate sol.top sol.crd Checking Unit. Building topology. Building atom parameters. For atom: .R.A Could not find type: HY For atom: .R
.A type OY Could not find perturbed type: HY Parameter file was not saved.
Atoms have names and types. Names are unique within the residue, and serve to distinguish the individual atoms (their topological positions) - e.g. H1'. Types are not unique - they are like a generalization of element to include (encode) information such as hybridization and bonded neighbors - e.g. amino hydrogen. The force field is essentially a definition of the properties of different atom types. These are all defined in the parm94.dat (new ff) or parm91X.dat (old ff). If you add a new type, you must define it - this is normally done in a frcmod file. However, one does not want to add new atom types to the force field unless absolutely necessary, since it means also generating bond, angle, and torsion parameters for the new type. I suspect that, especially in your case of hydrogen (HY), there may already an appropriate type that you could choose from the force field for the atom in its perturbed state. The best definition of atom types is probably the one on our web pages, since it was written specifically to be understandable at the undergrad level, with the help of Dr. Kollman.
If you do have to generate new types, see parameter generation, which is also in the appendix of the manual.
When leap is complaining about missing proper torsion parameters, the thing to do is _add_ parameters of the given multiplicity, normally the ones suggested (i.e. they will contribute 0 energy). Then there might be a second round of such msgs when you try to saveamberparmpert again. In this case, you _add_ some more parameters as before. Now saveamberparmpert should work. Do not _change_ any parameters in response to these msgs unless you understand why the params are there. I was trying to find out how to define the PMF-type perturbation option in LEaP, but I could not find it.
I have a dipeptide whose peptide bond will be changed from 0 to 180 degrees during a GIBBS run.
You should be able to
> saveamberparmpert molecule nullpert.top nullpert.crd
_without_ first defining any per-atom perturbations, and then define your PMF perturbation in the gibin file. This corresponds with the instruction for setting up a null perturbation topology file using parm, given in gibbs.doc's PMF section.