[gmx-users] pdb2gmx

[Valentina Erastova]

Hello all, 

I am converting a .pdb into .gro and .top and assigning ClayFF forcefield, that is not included in the gromacs.

It's a strange FF as doesn't have ones between all of the atoms, just O-H but it has an angle between a metal and OH, therefore I wore out molecule.rtp (see below) that included the angles, BUT wen I convert to the .top I only get bonds, but not angles (see below). Is there something I am missing or does gromacs not assign angles if no bonds are assigned?

Thank you!



molecule.rtp
[ B31 ] ;# ldh21 
  [ atoms ]
 ; atomname atomtype charge chargegroup
; charges were taken from paper by Kuang Wu and J R Schmidt; J Phys Chem C (2012)
; and edited to make it fir LDH31 model and produce +1
   o1  ohs  -1.113   0
   h1  ho     0.464   0
   o2  ohs  -1.113   0
   h2  ho     0.464   0
   o3  ohs  -1.113   0
   h3  ho     0.464   0
   o4  ohs  -1.113   0
   h4  ho     0.464   0
   mg1 mgo   1.403   0
   al1 ao    1.983   0
   o5  ohs  -1.113   0
   h5  ho     0.464   0
   o6  ohs  -1.113   0
   h6  ho     0.464   0
   o7  ohs  -1.113   0
   h7  ho     0.464   0
   o8  ohs   -1.113   0
   h8  ho     0.464   0
   mg2 mgo   1.403   0
   mg3 mgo   1.403   0
  [ bonds ]
 ; atom1 atom2   parametersindex
   o1 h1 ohs 
   o2 h2 ohs 
   o3 h3 ohs 
   o4 h4 ohs 
   o5 h5 ohs 
   o6 h6 ohs 
   o7 h7 ohs 
   o8 h8 ohs  
  [ angles ]
 ;  ai    aj    ak   gromos type 
mg1   o1   h1   moh
mg1   o8   h8   moh
mg1   o4   h4   moh
mg1   o6   h6   moh
mg1   o3   h3   moh
mg1   o5   h5   moh
al1   o3   h3   moh
al1   o5   h5   moh
al1   o2   h2   moh
al1   o7   h7   moh
al1   o4   h4   moh
al1   o6   h6   moh
mg2   o8   h8   moh
mg2   o2   h2   moh
mg2   o5   h5   moh
mg2   o4   h4   moh
mg2   o7   h7   moh
mg2   o1   h1   moh
mg3   o7   h7   moh
mg3   o1   h1   moh
mg3   o6   h6   moh
mg3   o3   h3   moh
mg3   o8   h8   moh
mg3   o2   h2   moh



ldh31.top
; Include forcefield parameters
#include "./ClayFF.ff/forcefield.itp"

[ moleculetype ]
; Name            nrexcl
Other               3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
; residue   1 B31 rtp B31  q +1.0
     1        ohs      1    B31     o1      1     -1.113         16   ; qtot -1.113
     2         ho      1    B31     h1      1      0.464      1.008   ; qtot -0.649
     3        ohs      1    B31     o2      1     -1.113         16   ; qtot -1.762
     4         ho      1    B31     h2      1      0.464      1.008   ; qtot -1.298
     5        ohs      1    B31     o3      1     -1.113         16   ; qtot -2.411
     6         ho      1    B31     h3      1      0.464      1.008   ; qtot -1.947
     7        ohs      1    B31     o4      1     -1.113         16   ; qtot -3.06
     8         ho      1    B31     h4      1      0.464      1.008   ; qtot -2.596
     9        mgo      1    B31    mg1      1      1.403      24.31   ; qtot -1.193
    10         ao      1    B31    al1      1      1.983      26.98   ; qtot 0.79
    11        ohs      1    B31     o5      1     -1.113         16   ; qtot -0.323
    12         ho      1    B31     h5      1      0.464      1.008   ; qtot 0.141
    13        ohs      1    B31     o6      1     -1.113         16   ; qtot -0.972
    14         ho      1    B31     h6      1      0.464      1.008   ; qtot -0.508
    15        ohs      1    B31     o7      1     -1.113         16   ; qtot -1.621
    16         ho      1    B31     h7      1      0.464      1.008   ; qtot -1.157
    17        ohs      1    B31     o8      1     -1.113         16   ; qtot -2.27
    18         ho      1    B31     h8      1      0.464      1.008   ; qtot -1.806
    19        mgo      1    B31    mg2      1      1.403      24.31   ; qtot -0.403
    20        mgo      1    B31    mg3      1      1.403      24.31   ; qtot 1

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1    ohs
    3     4     1    ohs
    5     6     1    ohs
    7     8     1    ohs
   11    12     1    ohs
   13    14     1    ohs
   15    16     1    ohs
   17    18     1    ohs

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

[ system ]
; Name
God Rules Over Mankind, Animals, Cosmos and Such

[ molecules ]
; Compound        #mols
Other               1