On Fri, Mar 18, 2011, Ilyas Yildirim wrote:
>
> One mistake I saw in people is that they disregard some important messages
> leap gives. Sometimes, when an original .pdb file is used to create the
> prmtop/inpcrd files, leap will add some extra heavy atoms and create the
> files accordingly. This happens when the naming of the atom is not
> recognized by leap. My rule of thumb is to play with the .pdb file until
> leap does not give any critical error messages (or weird messages like
> creating a new atom). In your .pdb file, I just kept the lines starting
> with ATOM, put TER cards when a sequence/strand is finished, and removed
> the water molecules. I would suggest you to do the same.
I just want to second what Ilyas says above. In the old days, hand-editing of
*every* pdb was virtually mandatory. Amber has become better at recognizing
things, but being careful at the initial stage is still excellent advice.
....dac
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Received on Sat Mar 19 2011 - 07:30:02 PDT
