> When I try to loadpdb, it says that it my
> structures have missing atoms which it adds.
> It then will not save the parameters when I
> use the saveAmberParm command.
This is probably because the atom naming scheme
in your pdb does not agree with amber's - not only
are the atoms added to replace the apparently
missing ones on loadpdb, but the unrecognized atoms
are added without atom types or charges since they
don't match the template.
The solution is either to use leap's atom name map
facility (see 'help' and/or default leaprc's), or
change the names in the pdb before loading.
Bill Ross
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Received on Wed Jun 26 2002 - 12:47:02 PDT
