On 6/4/13 12:05 PM, Valentina Erastova wrote:
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?


That's probably correct, given that normally pdb2gmx will build angles based on bonds that are present. Most "normal" usage will never have angles without bonds, so for now, you will have to write the angles in the topology yourself. I will file a bug report with a (much simpler) test case so we don't lose track of this issue. Given that it affects so few simulations, it may be a while before it is resolved, but it may well be worth doing simply for flexibility reasons.

-Justin

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--
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--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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