Re: [AMBER] Residue chirality

From: Karl N. Kirschner <>
Date: Mon, 15 Jul 2013 11:12:03 +0200 (CEST)

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,

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" <>
To: "AMBER Mailing List" <>
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...)


On Tue, 7/9/13, Karl N. Kirschner <> wrote:

 Subject: Re: [AMBER] Residue chirality
 To: "AMBER Mailing List" <>
 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.)
 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
 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 Mon Jul 15 2013 - 02:30:03 PDT
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