[gmx-users] How to make drug for OPLSA ff compatiable

Maik Goette mgoette at mpi-bpc.mpg.de
Thu Mar 16 11:40:10 CET 2006

Sorry, no.

I never worked on hemes or whatever FE is included.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

raja wrote:
> Thanks Mr. Goette, But error list is not so long , its simple as 
> Fatel error: atom type 'CR61' not found in the topology , where 'CR61'
> is the atom type occurs
> first in my drug itp file made from PRODRG.
> Otherwise could you suggest me any other forcefield otherthan OPLSA to
> treat Fe(II) in active site and also
> fix the drug atoms types compatiablity.
> With thanks,
> B.Nataraj
> On Thu, 16 Mar 2006 10:21:59 +0100, "Maik Goette"
> <mgoette at mpi-bpc.mpg.de> said:
>>You simply can't do that, right now.
>>OPLS isn't implemented into PRODRG, yet (correct me, if I'm wrong).
>>Therefore the atom-naming, etc. maybe wrong.
>>Anyway...a more detailed documentation of the error would be very
>>Maik Goette, Dipl. Biol.
>>Max Planck Institute for Biophysical Chemistry
>>Theoretical & computational biophysics department
>>Am Fassberg 11
>>37077 Goettingen
>>Tel.  : ++49 551 201 2310
>>Fax   : ++49 551 201 2302
>>Email : mgoette[at]mpi-bpc.mpg.de
>>         mgoette2[at]gwdg.de
>>WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
>>raja wrote:
>>>Dear GMXion,
>>>        I am now persuing simulation of drug-enzyme complex. I made
>>>        topology and gro file for drug using PRGDRG server. I am using
>>>        OPLSA force field for simulation since my protein having Fe(II)
>>>        at active site. I followed all steps based on drug-enzyme
>>>        simulation tutorial of gmx.  But still it shows error in grompp
>>>        step for "drug's atom types
>>>not found". I also updated the missing atom types of drugs in
>>>ffoplsaa.itp, ffoplsaanb.itp in share/top folder. but still the run
>>>shows the same error for new atom types in drug.itp file. 
>>>Any straight forward solution for this ?
>>>With thanks !
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