[gmx-users] regarding topology

[soumadwip ghosh]

Hi,
   I have a question about the topology made by SwissParam which is
compatible with CHARMM 27 force field. I hate to bring the same thing up
again and again but I am really doubtful about some of the parameters
created by the above mentioned web server. I have built a topology for
fullerene molecule using it at it looks like

[ moleculetype ]
; Name nrexcl
 LIG      3

[ atoms ]
; nr type resnr resid atom cgnr charge mass
   1 CB   1  LIG C       1  0.0000  12.0110
   2 CB   1  LIG C1      2  0.0000  12.0110
   3 CB   1  LIG C2      3  0.0000  12.0110
   4 CB   1  LIG C3      4  0.0000  12.0110
   5 CB   1  LIG C4      5  0.0000  12.0110
   6 CB   1  LIG C5      6  0.0000  12.0110
   7 CB   1  LIG C6      7  0.0000  12.0110
   8 CB   1  LIG C7      8  0.0000  12.0110
   9 CB   1  LIG C8      9  0.0000  12.0110
  10 CB   1  LIG C9     10  0.0000  12.0110
  11 CB   1  LIG C10    11  0.0000  12.0110
  12 CB   1  LIG C11    12  0.0000  12.0110
  13 CB   1  LIG C12    13  0.0000  12.0110
  14 CB   1  LIG C13    14  0.0000  12.0110
  15 CB   1  LIG C14    15  0.0000  12.0110
  16 CB   1  LIG C15    16  0.0000  12.0110
  17 CB   1  LIG C16    17  0.0000  12.0110
  18 CB   1  LIG C17    18  0.0000  12.0110
  19 CB   1  LIG C18    19  0.0000  12.0110
  20 CB   1  LIG C19    20  0.0000  12.0110
  21 CB   1  LIG C20    21  0.0000  12.0110
  22 CB   1  LIG C21    22  0.0000  12.0110
  23 CB   1  LIG C22    23  0.0000  12.0110
  24 CB   1  LIG C23    24  0.0000  12.0110
  25 CB   1  LIG C24    25  0.0000  12.0110
  26 CB   1  LIG C25    26  0.0000  12.0110
  27 CB   1  LIG C26    27  0.0000  12.0110
The parameters are properly placed in the latter part (kb, force
constant, fu th0 kth ub0 kub th0 kth ub0 kub and so on) in appropriate
directives [ angles ], [ dihedrals ] etc. But the CB atomtype does not
exist as such in the CHARMM 27 ff directory. So how will the atomic
interactions are validated in this case. I am stuck with this problem for a
long time since I generally
1. draw the structure in gaussview 09
2. save it as mol2 file
3. Upload it on SwissParam web server to obtain topology.

Is there anything wrong happening or is there some trivial point I'm
missing out here? At the end of the day, my simulations do run without any
hitch but I struggle to get the desired molecular interaction most of the
time. Is it because the atomtype description itself is vague here and does
not belong to CHARMM 27 ?

If this is indeed the problem, I am thinking of switching over to ParamChem
in order to access CGenFF parameters.

Any kind of help will be hugely appreciated.

Regards,
Soumadwip
IITB
India