On Mon, Mar 07, 2022, Alysia Mandato wrote:
>
>*/ihome/crc/build/amber/amber20_build-GNU/bin/teLeap: Error!Could not find
>bond parameter for: O2 - Ag+
Are you expecting to have a bond between and oxygen and silver? (That is
possible, but most monovalent ions use a non-bonded model.)
Amber has standard parameters for AG (loaded in conjuction with
leaprc.water.tip3p), so you should be able to just load a proper PDB file.
Maybe you could attach the relevant portion of your 4wlw_corrected.pdb file.
(There should be no need to have createAtom and createResidue commands,
etc., unless you really know that you don't want the standard parameters.)
...hope this helps...dac
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Received on Mon Mar 07 2022 - 13:00:02 PST
