Re: [AMBER] Residue chirality

From: Krisztina Feher <>
Date: Tue, 16 Jul 2013 13:20:33 -0700 (PDT)

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!


On Mon, 7/15/13, Karl N. Kirschner <> wrote:

 Subject: Re: [AMBER] Residue chirality
 To: "AMBER Mailing List" <>
 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
 Best regards,
 Title: Novel Simulation Approaches for Polymeric and Soft
 Matter Systems
 Author(s): Cerda, Joan J.; Holm, Christian; Kremer, Kurt
 20   Issue: 7   Special Issue:
 SI   Pages: 444-445
 Title: Temperature and Pressure Dependence of Polystyrene
 Dynamics through Molecular Dynamics Simulations and
 Author(s): Harmandaris, Vagelis A.; Floudas, George; Kremer,
 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
 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
 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,
 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,
 Izvekov, S. & Voth, G. A. Modeling real dynamics in the
 coarse-grained representation of condensed phase systems
 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
 On Tue, 7/9/13, Karl N. Kirschner <>
  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,
  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,
  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
  and -118.5 (PMD).
    Unless I am missing something, this shows that PMD
  had its chirality altered by xleap. Granted, that I may
  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
  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
  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
  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 compute the
> chirality dihedral angles and obtain both positive
  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 16 2013 - 13:30:03 PDT
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