[gmx-users] FEP : separating components of dgdl
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.
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