Re: [AMBER] Residue chirality

From: Karl N. Kirschner <>
Date: Tue, 9 Jul 2013 17:27:48 +0200 (CEST)

Hi Carlos and Jason,

  I ran into this problem when I was working on a model for creating a short strand of PMMA polymer several years ago. (Granted, not something that Amber was originally created to handle.) Since these residues were nonstandard, I built my own prep files and linked them together in xleap using the sequence command, as one would do for a peptide.

  When I measure the prep file's improper torsion angle around the chiral center using the measureGeom command, for one residue (PMD) I obtain a value of +119.5, and for the other (PML) I obtain -119.5.

  When I do the same measurement, but now one the short "polymer" (BEG-PML-PMD-END), I obtain values of -118.5 (PML) and -118.5 (PMD).

  Unless I am missing something, this shows that PMD had its chirality altered by xleap. Granted, that I may have introduced an error into the prep files, but I have triple checked them. Also note that if I were to save the BEG-PML-PMD-END as a pdb file, and opened it up in an external viewer, there are incorrect bonds added to the molecule due to inappropriate short distances-- so I know that the prep files are not conformationally optimized for the sequence command. Not really knowing the leap code, I still didn't expect the change in chirality.

  All of this was done using: "Latest patch applied to AmberTools12: 31". The leap input and part of the log file are included below. If you see something obvious in my thoughts or the leap input, I would appreciate hearing it. (I personally do not need this example to be solved, and I use it only for demonstrating what I encountered before.)


leap input:
logfile leap.log
source leaprc.ff99SB

loadAmberPrep BEG.prep
loadAmberPrep PML.prep
loadAmberPrep PMD.prep
loadAmberPrep END.prep

poly = sequence {BEG PML PMD END}

measureGeom PML.1.C4 PML.1.C5 PML.1.C3 PML.1.C2
measureGeom PMD.1.C4 PMD.1.C5 PMD.1.C3 PMD.1.C2

measureGeom poly.2.C4 poly.2.C5 poly.2.C3 poly.2.C2
measureGeom poly.3.C4 poly.3.C5 poly.3.C3 poly.3.C2

> measureGeom PML.1.C4 PML.1.C5 PML.1.C3 PML.1.C2
Torsion angle: -119.48 degrees
> measureGeom PMD.1.C4 PMD.1.C5 PMD.1.C3 PMD.1.C2
Torsion angle: 119.50 degrees

> measureGeom poly.2.C4 poly.2.C5 poly.2.C3 poly.2.C2
Torsion angle: -118.47 degrees
> measureGeom poly.3.C4 poly.3.C5 poly.3.C3 poly.3.C2
Torsion angle: -118.47 degrees

----- Original Message -----
From: "Carlos Simmerling" <>
To: "AMBER Mailing List" <>
Sent: Tuesday, July 9, 2013 2:06:05 PM
Subject: Re: [AMBER] Residue chirality

I've done this in tleap many times and it does work. The issue here is
probably in the details. What was the old a new sidechain? What is nearby?
When leap built it, did it fit without clash? Was the chivalry wrong coming
from leap, or after some minimization?

Note that leap can do this, but it won't try to optimize the location. In
most cases you probably want to use a different program to build initial
structures, not leap. Swisspdb does a reasonable job of sidechain
On Jul 9, 2013 5:25 AM, "Karl N. Kirschner" <>

> Hi,
> At one time there was a bug concerning this in tleap (and g/sleap??),
> and I am not sure if it was ever corrected. If I recall correctly, the only
> work-around I found was to construct the enantiomer using an external
> editor (e.g. PyMol) and load it into xleap. This preserved the connectivity
> and dihedral angles.
> Cheers,
> Karl
> ----- Original Message -----
> From:
> To:
> Sent: Tuesday, July 9, 2013 11:07:58 AM
> Subject: [AMBER] Residue chirality
> Hello,
> I try to perform mutations on a peptide by removing the sidechain atoms
> and replacing the old residue names with new residue names, then letting
> tleap add in the missing atoms. I check the chirality of the residues and
> find out that I don't have the correct chirality (i.e., I compute the
> chirality dihedral angles and obtain both positive and negative numbers).
> Is there any better way to do mutations with Amber/tleap? How can I fix
> the incorrect chirality?
> Thank you,
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Received on Tue Jul 09 2013 - 08:30:03 PDT
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