Re: [AMBER] free energy calculation and leap error

From: David A Case <>
Date: Tue, 22 Oct 2019 14:20:23 -0400

On Tue, Oct 22, 2019, Sadaf Rani wrote:

>Loading PDB file: ./ala2_2.pdb
>Warning: name change in pdb file residue 3 ;
> this residue is split into ALA and NME.
>1 residues had naming warnings.
> There are split residues;
> residue sequence numbers will not correspond to those in the pdb.

Look closely at what is in ala2_2.pdb: something is wrong with the
residue names or numbers. Once you see what has happened, that may help
in figuring out what happened. (You have a very complex workflow: is
there any part of this you can do by hand?)


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Received on Tue Oct 22 2019 - 11:30:03 PDT
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