[gmx-users] FEP : separating components of dgdl

Maik Goette mgoette at mpi-bpc.mpg.de
Tue Feb 5 09:24:29 CET 2008


This warning is really strange.
You could try to execute grompp with -pp to get the preprocessed 
topology and have a look, if the the B-parameters are included 
correctly. As far as I know, it should; I do it the same way.
Anyway, you could also explicitly take the parameters for that dihedral 
from the forcefield and write them in the topology.
BTW, in your case its not problematic anyway, cause they are the same :)


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/

BON Michael wrote:
> Thanks Maik for your parameters for amber99 soft core !
> Berk, you were right. The missing term is indeed the one associated to the use of constraints=all-bonds. And yes, there was a mistake in my .top file...
> May I ask an other question ?
> I still have a warning message with grompp : 
> "WARNING 1 [file "XXX.itp", line 3451]:
>    Some parameters for bonded interaction involving perturbed atoms are specified
>    explicitly in state A, but not B - copying A to B"
> where as the line 3451 is  (dihedral) : 
> 175 177 178 187  1 nucleic_imp_10  nucleic_imp_10
> nucelic_imp_10 being defined in ffamber99bon.itp. 
> It seems to me that the state B is explicitly specified. How to get rid of this warning ? It does what I want anyway, but I want to understand what is happening.
> Thanks, 
> Michaël Bon
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