AMBER Archive (2009)

Subject: [AMBER] Loading PDB of complex

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Thu May 21 2009 - 08:13:36 CDT

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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