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

From: James Starlight <>
Date: Fri, 4 Aug 2017 20:50:25 +0200

BTW could someone help me with the scripting of such CAPPING?
For the pdb I need to 1) find the string where the 3rd column = OXT,
change it to N and the residue name (4 column to NHE), and also the
last column from O to N; 2) change the next string to TER

I tried to use

awk '$3=="OXT"{ f=1; rn=NR; $3=$NF="N"; $4="NHE" }/TER/ && f && NR-rn
== 1{ $0=$1 }1' file.pdb

it produce correct substitution, however put only one spacing between
columns of new string like:

ATOM 2410 N NHE 299 -17.563 -15.711 -15.915 1.00 76.42 N

thus producing broken pdb file. How to present the original format?

ATOM 2448 N NHE 301 -6.821 36.580 65.884 1.00 19.70 N



2017-08-04 14:34 GMT+02:00 James Starlight <>:
> 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
> James
> 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 - 12:00:02 PDT
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