[gmx-users] FEP : separating components of dgdl

BON Michael michael.bon at cea.fr
Mon Feb 4 16:18:53 CET 2008

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.

Michaël Bon
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