multiple dihedrals in Charmm topology files

Mary Susan Cates mscates at bioc.rice.edu
Mon Feb 7 15:55:33 EST 2000


    We are using xplor 3.851 to generate .psf files for molecular
dynamics simulations in NAMD.  The topology file is from the charmm22
subdirectory in the xplor toppar directory, topallh22x.pro.  We have
noticed that this topology file lists the peptide bond dihedral twice,
and causes the .psf file to list this dihedral twice in the
connectivity.
    Under PRESidue PEPT, the peptide bond dihedral appears this way:

      ADD DIHEdral  -CA   -C    +N    +CA    ! multiple dihedral
      ADD DIHEdral  -CA   -C    +N    +CA    ! multiple dihedral

This is also true for our version of xplor 3.1, so I don't think it's
likely that someone here edited these files to contain this dihedral
twice, I think it must have come to us this way.  In 3.851 there are
also several sidechains that have multiple dihedrals listed; ie, serine:



      BOND  CA    HA
      BOND  CB    HB1
      BOND  CB    HB2
      BOND  OG    HG1

      DIHEDRAL CA  CB  OG  HG1 ! multiple dihedral
      DIHEDRAL CA  CB  OG  HG1 ! multiple dihedral
      DIHEDRAL CA  CB  OG  HG1 ! multiple dihedral

Do you know the rationale for listing these dihedrals more than once?

Thanks,


           M. Susan Cates
  ^-^      Dept. of Biochemistry
 (o o)     Rice University         Ph. 713-348-3346
 ( V )     Houston, TX 77005       FAX 713-285-5154
--m-m-------Internet:http://www.bioc.rice.edu/~mscates---------------


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