Re: [AMBER] A bug with unperturbed charge during tleap processing

From: James Starlight <>
Date: Fri, 4 Aug 2017 14:34:02 +0200

Yep that's right! (sorry i am stupid)
So the problem just disapears if I
1) remove OXT in pdb (the tleap than add it back without error)
2_ substitute OXT for N of NHE (add peptide bond of cap) - tleap again
add everything back.

The same for all pdbs prepared by Modeller


2017-08-04 14:04 GMT+02:00 David A Case <>:
> On Fri, Aug 04, 2017, James Starlight wrote:
>> Yep it was the C-term residue and the TER was present
> Then something strange is happening. We would need to see a minimal example
> that illustrates the problem. Try to see what is different about your
> protein PDB (or tleap input commands) compared to standard examples that
> don't exhibit this problem.
>> So to fix the issue I made a script which changes OXT of last residue
>> to N of NHE (add NHE to cap C term)
>> and also change N of the first residue to C of ACE (tleap than add
>> back N for the adjacent residue and surprisingly fixed steric clashes
>> between N and C of ACE). I checked in VMD the new peptide bonds look
>> fine.
>> There is no bugs with charges and any warning. Total charge of the
>> system =0 after its neutralization. BUT total charge of the system
>> has not been changed compared to uncapped case....
> Sounds exactly like what one expect, does it not? If you neutralize both
> the N- and C-terminal residues, then the total charge of the protein/peptide
> will not change.
> ....dac

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Received on Fri Aug 04 2017 - 06:00:05 PDT
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