[gmx-users] pdb2gmx - .top missing values

[Dallas Warren]

Just thought I should provide some further information ....

Here is some sections of what I have added to the .rtp file ....

[ CHD ]
  [ atoms ]
; name  type  charge chargegroup
    C18   CH3   0.000     0
    C13    CB   0.000     1
    C12   CH1   0.150     2
    O12    OA  -0.548     2
    H12    HO   0.398     2
......
  [ bonds ]
;atom1 atom2
    C18   C13
    C13   C12
    C13   C14
    C13   C17
    C12   O12
    O12   H12
.........

There is nothing specifically defined in terms of bonds etc.  This I was 
assuming that it would pull from the ff*nb.itp file.

When I process the pdb file for this residue, this is what the .top file 
looks like ......

..................
[ moleculetype ]
; Name            nrexcl
Protein             3

[ atoms ]
;   nr       type  resnr 
residue  atom   cgnr     charge       mass  typeB    chargeB      massB
      1        CH3      1    CHD    C18      1          0     15.035   ; qtot 0
      2         CB      1    CHD    C13      2          0     12.011   ; qtot 0
      3        CH1      1    CHD    C12      3       0.15     13.019   ; 
qtot 0.15
      4         OA      1    CHD    O12      3     -0.548    15.9994   ; 
qtot -0.398
      5         HO      1    CHD    H12      3      0.398      1.008   ; qtot 0
......................
[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
     1     2     1
     2     3     1
     2    22     1
     2    25     1
     3     4     1
.................
[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
     1     4     1
     1     6     1
     1    21     1
     1    23     1
     1    24     1
..................
[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
     1     2     3     1
     1     2    22     1
     1     2    25     1
     3     2    22     1
     3     2    25     1
................
[ dihedrals ]
;  ai    aj    ak    al 
funct            c0            c1            c2            c3            c4 
            c5
     1     2     3     4     1
     1     2    22    21     1
     1     2    25    24     1
     2     3     4     5     1
     2     3     6     7     1
...................
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
.....................

Therefore it gets correct where all the bonds are, angles etc.  However, it 
has left out the details of how long they are, force constants etc.  As I 
said in the previous email, I assumed that these would all be inserted into 
the .top file to then be subsequently used by the rest of the software.  If 
this isn't the case, then I don't actually have a problem at all then, was 
just expecting something else.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
dallas.warren at vcp.monash.edu.au
+61 3 9903 9076
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