[gmx-users] on atomtypes

Brett brettliu123 at 163.com
Thu May 12 17:17:50 CEST 2016

Dear All,

Following is the part of the atomtypes.atp  for gromos54a7:

    O  15.99940 ;     carbonyl oxygen (C=O)
   OM  15.99940 ;     carboxyl oxygen (CO-)
   OA  15.99940 ;     hydroxyl, sugar or ester oxygen
   OE  15.99940 ;     ether or ester oxygen
   OW  15.99940 ;     water oxygen
    N  14.00670 ;     peptide nitrogen (N or NH)
   NT  14.00670 ;     terminal nitrogen (NH2)
   NL  14.00670 ;     terminal nitrogen (NH3)
   NR  14.00670 ;     aromatic nitrogen
   NZ  14.00670 ;     Arg NH (NH2)
   NE  14.00670 ;     Arg NE (NH)
    C  12.01100 ;     bare carbon
  CH0  12.0110  ;     bare sp3 carbon, 4 bound heavy atoms
  CH1  13.01900 ;     aliphatic or sugar CH-group
  CH2  14.02700 ;     aliphatic or sugar CH2-group
  CH3  15.03500 ;     aliphatic CH3-group
  CH4  16.04300 ;     methane
 CH2r  14.02700 ;     CH2-group in a ring

If I need to insert a new type list for example HS14 with weight 1.0080, should the word description of the atomtype (for example, "CH2-group in a ring" for "CH2r  14.02700") should be accurate or just a kind of reminder which the gromacas will not read?

In addition, the atomtypes.atp is a readonly file in /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/. WIll you please let me know how to save it after the HS14 atomtype was added?


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