[gmx-users] How to make drug for OPLSA ff compatiable
mgoette at mpi-bpc.mpg.de
Thu Mar 16 11:40:10 CET 2006
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
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/
> 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,
> 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
>>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/
>>> 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 !
>>gmx-users mailing list gmx-users at gromacs.org
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-request at gromacs.org.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users