[gmx-users] Question about topology construction.

sujithkakkat . sujithks58 at gmail.com
Thu Mar 20 15:21:31 CET 2014


  I am using gromacs-4.6.5. For the sake of practice,  I made a .itp file
for carbon dioxide based on the EMP2 model (J.Phys.Chem 1995, 99,
12021-12024) .

  The file is self-contained with all parameters including the [default]
and [atomtypes].

 I tried to do run a simulation on a system containing only CO2 molecules.
My topology file included only the .itp which I made and no other
forcefield.itp is included. (Is it ok to do so?)

 When I try to generate .tpr for an energy minimization, I get the error
"Found a second defaults directive" which the manual says is due to second
defaults being set in an included topology file.

BUT,   Here I am defining  'default' only once, which is in the .itp file
for CO2 which I made and no other .itp from any forcefield is included. So
I am not sure how it is the "second" default  and what is causing the
error. Is it necessary that the .itp should be included in some forcefield
directory although it has all the parameters, and then include it into .top
as a subset of the forcefield?

Please let me know what you think.

Have a look at the .itp I made for CO2 and please let me know if anything
is seriously wrong.

  [ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
   1                     3               no                1.0         1.0

; name        mass        charge     ptype    sigma    epsilon
   CA        12.01100      0.6512       A      0.2757   0.2339
   CO        15.99940     -0.3256       A      0.3033   0.6695

; name  nrexcl
  CO2    1

; nr    type    resnr   residue    atom    cgnr   charge    mass
  1      CA       1      CO2        CA       1     0.6512    12.0110
  2      OC       1      CO2        OC1      1    -0.3256    15.9994
  3      OC       1      CO2        OC2      1    -0.3256    15.9994

; i   j   funct    doc
  1   2     1      0.1149
  1   3     1      0.1149

1    2    3
2    1    3
3    1    2

; i   j   k   funct   a0   ak
  1   2   3     1     180  1236



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