If you don't know what a chain type is, you can't be affected by them.
It's a legacy thing.
Bill
David Winogradoff <dwino218.gmail.com> wrote:
> Dear amber community,
>
> I am acetylating a lysine in my PDB using xLeap by adding an "ACE." When I
> finish editing the file and execute "saveamberparm," xLeap creates the
> .prmtop and .inpcrd files but provides the following message:
>
> Building Topology
> .
> . #normal messages
> .
> Building H-Bond parameters
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
>
> res total affected
>
> ACE 1
> CGLN 1
> NSER 1
> )
> (no restraints).
>
> It looks to me like amber doesn't like something about the residues at the
> 2 termini (SER and GLN) and the acetyl group that I have added, ACE.
>
> Will this have an effect on dynamics? Or is this a message I can safely
> ignore?
>
> Thank you,
> David Winogradoff
> ~~~~~~~~~~~~~~~~~~~~~~~~
> Research Assistant
> Chemical Physics
> University of Maryland
> College Park
> ~~~~~~~~~~~~~~~~~~~~~~~~
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Received on Tue Feb 11 2014 - 22:00:02 PST
