You have to rename atoms and residues to match AMBER convention.
To find the right name, try to generate a small box with tleap.
Inspecting the so created file, you can find the right names.
Il 12/04/2011 09:09, MD ha scritto:
>
> Hi All,
>
> I get a .pdb from Gromacs, the .pdb is 4x4x1.1 water and the density is OK (about 1g/cc), but when i load this .pdb to leap, it said 'created a new atom named: HW1 within residue: .R<SOL 226>'
>
> i need to modify ... how can i let AMBER know the .pdb?
> I can see this .pdb using VMD, and it is very good to see.
>
> Hope someone can help me
>
> Thanks
>
>
>
>
>
>
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Received on Tue Apr 12 2011 - 01:30:02 PDT
