AMBER Archive (1999)

Subject: Re: atom types

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Dec 07 1999 - 16:15:30 CST

        I would like convert atoms from Macromodel to AMBER format.
        Simply creating a PDB in Macromodel and reading the PDB
        file via xLeap doesn't create the proper atom types for AMBER.

There appears to be a fundamental misconception here:
atom types are not in pdb files. If all the residues
used are in the standard force field, all you need to
do is ensure either that

 - atom and residue _names_ match those in the residue
   templates in the force field

or

 - atom and residue name mappings are supplied to leap
   so that it can convert.

If, on the other hand, you have a lot of nonstandard residues,
then you must create your own templates for these residues,
including assigning type and charge to each atom and supplying
any vdw, bond, angle, torsion and improper torsion parameters
required by these types - see amber the web page on developing
new parameters in this case.

Bill Ross