> My questions are: Should I change the labels coming from the PDB (HOH) to
> AMBER's (ex. HW1, OW, HW2) for it to work?. If I do this, then, Is it OK
> to assume that these water molecules will take the WT3 potential?. What
> could be the impact of this action in the calculation?.
If you are using leap, you must either change residue & atom
names to agree w/ the template for WAT, or use addPdbResMap and
addPdbAtomMap to convert them on input -- provided that you
want to use the TIP3 potential. If you want to use another
potential, you need to either make a template for it, in which
case the residue/atom names are your choice, or you can use a
frcmod to change TIP3 potentials, if your new potential also
uses an H-H bond to enforce rigidity.
Bill Ross
Received on Tue Jun 29 1999 - 13:55:20 PDT
