[gmx-users] Problem with Atom type

[Dastmalchi]

Hi GMX users,

I am dealing with a system which has a Molybdenum-containing cofactor in it. I have written a "itp" file for this cofactor, and included that in my top file and tried to use it, but I am getting error, saying that it can't find the atom type 'MO' for the grompp command.
Here is the few last line of the message:

Processing topology .

Generated 1125 of the 1326 nonbonded parameter combination

Cleaning up temporarily file grompp001302

Fatal error: atom type 'MO' not found! 



I have named the molybdenum atom MO and have added the following line into atommass.dat files:
??? MO 95.9400
I have also added a line into ffgmx.atp file:
MO 95.94000 ; molybdenum
At the end of email I have put the content of the itp file for the cofactor called MOS.

1) Would you please let me know if the itp file is OK? I didn't add any values for bonds, angles and dihedrals. Are those info necessary?

2) Is there any further changes that I need to do? i.e. to add a necessary info into a particular file.


Many thanks for your help.

Cheers, Saivoush



[ moleculetype ]
;name nrexcl
MOS 3
[ atoms ]
; nr type resnr resid atom cgnr charge
1 MO 1 MOS MO  1 0.474
2  S 1 MOS S   1 -0.125
3 OA 1 MOS O1  1 -0.397
4 OA 1 MOS O2  1 -0.372
5 HS 1 MOS HAA 1 0.199
6 HS 1 MOS HAB 1 0.221
[ bonds ]
;ai aj fu 
1 2 1 
1 3 1
1 4 1 
3 5 1 
4 6 1
[ angles ]
;ai aj ak fu 
2 1 3 1 
2 1 4 1 
1 3 5 1 
1 4 6 1 
3 1 4 1 
[ dihedrals ]
;ai aj ak al fu 
2 1 3 5 1 
2 1 4 6 1 
5 3 1 4 1 
6 4 1 3 1 
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