Super!
Thanks for your reply.
Happy New Year!
Jim Kress
-----Original Message-----
From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Sent: Sunday, December 31, 2023 9:16 AM
To: jimkress_58.kressworks.org; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] tleap output question
HI James,
NPRO and CGLU simply indicate you have N-terminal Pro and C-termianl Glu
residues (one each). You can go ahead and run dynamics. The system built
without errors, warnings, or notes.
Best,
Matthew
> On Dec 31, 2023, at 1:15 AM, James Kress via AMBER <amber.ambermd.org>
wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> When running tleap to process a protein, I get the following results at
the end of the run:
>
>> saveamberparm ewsfli1 ewsfli1_noNaCl.prmtop ewsfli1_noNaCl.inpcrd
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 243 improper torsions applied
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
> 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
>
> CGLU 1
> NPRO 1
> WAT 29492
> )
> (no restraints)
>> quit
> Quit
>
> Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
>
> I do not know what to do about the:
>
> CGLU 1
> NPRO 1
>
> Information. What does this mean and how do I deal with it?
>
> The Building Protein Systems in Explicit Solvent tutorial indicates that,
after running H++, the AMBER compatible PDB (PQR) structure in predicted
protonation state should be examined and GLU should be replaced with GLH.
Is that what needs to be done about the CGLU output?
>
> What about the NPRO output?
>
> All suggestions appreciated. If additional information is required, I'd
be happy to provide it.
>
> Happy New Year!
>
> Jim Kress
>
>
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Received on Sun Dec 31 2023 - 14:00:02 PST
