AMBER Archive (2009)

Subject: Re: [AMBER] Loading PDB of complex

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu May 21 2009 - 08:48:06 CDT

look in your pdb file- do you actually have 2 atoms with that name in
that residue?

On Thu, May 21, 2009 at 9:13 AM, Vikas Sharma
<vs_vikassharma_at_yahoo.co.in> wrote:
> 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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