Dear All,
i am using Amber10..
i opened xleap and loaded ff03 and gaff..then i loaded tyhe prepin and frcmod file of the ligand...
then i saved the .prmtop and .inpcrd for the protein alone..
and when i try to load the pdb file of the complex (protein along with the ligand) i got the "bondatomproblem" error...to rectify the error i manually changed the pdb...
the when i try to load the pdb of the complex(protein + ligand), it gives the message:
Residue 222: duplicate [H 6] atoms (total 2)
warning : Atoms name in each residue should be unique....
and after this there is no problem when i neutralize and solvate the complex and save the prmtop and inpcrd files...
Is there any problem???
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Received on Thu May 21 2009 - 08:38:13 PDT
