Hi Karl,
Thanks a lot for this detailed information! The polymer in my case might not have so much mobility as it is a crosslinked polistyrene resin and as a first attempt we would like to see if there might be any sort of interaction between the resin and the attached peptide. I have no idea if anyone have tried to tackle such system and, frankly, I am new to this area, so I should certainly read the papers first. Thanks again!
best,
Krisztina
--------------------------------------------
On Mon, 7/15/13, Karl N. Kirschner <kkirsch.scai.fraunhofer.de> wrote:
Subject: Re: [AMBER] Residue chirality
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Monday, July 15, 2013, 11:12 AM
Hello Krisztina,
I did an atomistic simulation on a isotactic and
atatic poly(methyl methacrylate) (PMMA) melt using Amber
(DOI:10.1080/08927020903536374). The force field used in the
study was a simple extension of Glycam06. While intended for
carbohydrates modeling, Glycam06 was originally developed
and optimized using simple organic compounds and is fairly
transferable. This extension was the foundation for
developing a larger force field for modeling
lipopolysaccharide membranes (DOI: 10.1021/ct300534j).
However, atomistic simulation of polymer melts is not
the best way to study these systems, as I have learned. The
problem is in getting conformational sampling and the long
simulation time needed due to long auto-correlation times.
There are methods to get around this, including forward and
back mapping between atomistic and coarse-grained models.
Many of the polymer simulations are done at the mesoscale
using coarse-grained models.
When I was learning about this area, I found the
research by Drs. Kurt Kremer and Florian Mueller-Plate to be
enlightening. If you are interested in this area take a look
at the articles and research groups I give below - they
should get you started on uncovering more polymer modeling
literature.
Best regards,
Karl
Title: Novel Simulation Approaches for Polymeric and Soft
Matter Systems
Author(s): Cerda, Joan J.; Holm, Christian; Kremer, Kurt
Source: MACROMOLECULAR THEORY AND SIMULATIONS Volume:
20 Issue: 7 Special Issue:
SI Pages: 444-445
Title: Temperature and Pressure Dependence of Polystyrene
Dynamics through Molecular Dynamics Simulations and
Experiments
Author(s): Harmandaris, Vagelis A.; Floudas, George; Kremer,
Kurt
Source: Macromolecules Volume: 44 Issue: 2 Pages: 393-402
Published: JAN 25 2011
Title: Fine-graining without coarse-graining: an easy and
fast way to equilibrate dense polymer melts
Author(s): CARBONE, P; KARIMI-VARZANEH, HA; MULLER-PLATHE, F
Source: FARADAY DISCUSSIONS Volume: 144 Pages: 25-42
Published: 2010
Title: Molecular dynamics simulations of polyaminoamide
(PAMAM) dendrimer aggregates: molecular shape, hydrogen
bonds and local dynamics
Author(s): CARBONE, P; MULLER-PLATHE, F Source: SOFT MATTER
Volume: 5 Issue: 13 Pages: 2638-2647 Published: 2009
Apel, U. M.; Hentschke, R. & Helfrich, J. Molecular
Dynamics Simulation of Syndio- and Isotactic Poly(methyl
methacrylate) in Benzene Macromolecules, 1995, 28,
1778-1785
Ghanbari, A.; Boehm, M.C.; Mueller-Plathe, F. A Simple
Reverse Mapping Procedure for Coarse-Grained Polymer Models
with Rigid Side Groups
Macromolecules 2011, 44, 5520-5526
Depa, P. K. & Maranas, J. K. Speed up of dynamic
observables in coarse-grained molecular-dynamics simulations
of unentangled polymers JOURNAL OF CHEMICAL PHYSICS, 2005,
123
Izvekov, S. & Voth, G. A. Modeling real dynamics in the
coarse-grained representation of condensed phase systems
JOURNAL OF CHEMICAL PHYSICS, 2006, 125
Okada, O.; Oka, K.; Kuwajima, S. & Tanabe, K. Molecular
dynamics studies of amorphous poly(tetrafluoroethylene)
MOLECULAR SIMULATION, 1999, 21, 325-342
Paul, W. & Smith, G. D. Structure and dynamics of
amorphous polymers: computer simulations compared to
experiment and theory REPORTS ON PROGRESS IN PHYSICS, 2004,
67, 1117-1185
Wu, C. & Xu, W. Atomistic molecular modelling of
crosslinked epoxy resin Polymer, 2006, 47, 6004-6009
Wunderle, B.; Dermitzaki, E.; Hoelck, O.; Bauer, J.; Walter,
H.; Shaik, Q.; Raetzke, K.; Faupel, F.; Michel, B. &
Reichl, H. Molecular dynamics approach to structure-property
correlation in epoxy resins for thermo-mechanical lifetime
modeling Microelectronics Reliability, 2010, 50, IEEE CPMT;
Nokia; NXP Semiconductors; Robert Bosch GmbH; Siemens
Yarovsky, I. & Evans, E. Computer simulation of
structure and properties of crosslinked polymers:
application to epoxy resins Polymer, 2002, 43, 963-969
----- Original Message -----
From: "Krisztina Feher" <feher_krisztina.yahoo.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Sunday, July 14, 2013 9:50:17 AM
Subject: Re: [AMBER] Residue chirality
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,
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
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>
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>
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Received on Tue Jul 16 2013 - 13:30:03 PDT
