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

From: James Starlight <>
Date: Fri, 4 Aug 2017 09:19:27 +0200

Yep it was the C-term residue and the TER was present

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

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 O_O although there is
no no Cterminal and Nterminal residues in present topology, assuming
that both of them should be neutral. Does the ACE and NHE are indeed
neutral terms ?


2017-08-04 3:07 GMT+02:00 David A Case <>:
> On Thu, Aug 03, 2017, James Starlight wrote:
>> FATAL: Atom .R<PHE 299>.A<OXT 21> does not have a type.
> Amber doesn't realize that residue 299 is a terminal residue (becuase then
> it would call it CPHE internally.) If 299 should be a C-terminal residue,
> be sure to put a TER card after it in the input pdb file. If it is not
> a C-terminal residue, then the OXT atom is out of place.
> ....dac
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Received on Fri Aug 04 2017 - 00:30:03 PDT
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