Hi Karl,
Sorry for the diversion of the topic, but I got curious: did you use AMBER for an organic polymer? With which forcefield? Do you know any description of such simualtions in the literature? (I did some searches, but so far did not find any...)
regards,
Krisztina
--------------------------------------------
On Tue, 7/9/13, Karl N. Kirschner <kkirsch.scai.fraunhofer.de> wrote:
Subject: Re: [AMBER] Residue chirality
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Tuesday, July 9, 2013, 5:27 PM
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.)
Bests,
Karl
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
leap.log:
---------
> 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" <carlos.simmerling.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
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
placement.
On Jul 9, 2013 5:25 AM, "Karl N. Kirschner" <kkirsch.scai.fraunhofer.de>
wrote:
> 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: tdo.chem.ucsb.edu
> To: amber.ambermd.org
> 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 Sun Jul 14 2013 - 01:00:02 PDT
