From your mails, your problem is not yet clear. I only understand that you are using interface to Gaussian and using Gromos ff.
Is the problem is to create of an appropriate QM system by Gromacs interface and it is related to the use of Gromos united atom ff which removes the non-polar hydrogens? I don't see any problem with your index.ndx and with the size of the QM system. Also, from my communication with Gerrit, who developed the Gaussian interface, I understood that there should not be any problem with Gaussian interface to QM/MM while one is using the Gromos united atom ff. If you can more specific about the problem, we can try to solve.
regards,
pb.
On Aug 2, 2006, at 12:34 PM, Antonio Sergio Kimus Braz wrote:
Hi--
QM options used are :
QMMM = yes
QMMM-grps = QMatoms
QMmethod = CASSCF
QMbasis = 3-21G
QMMMscheme = normal
QMcharge = -1
CASelectrons = 6
CASorbitals = 6
SH = yes
if you desire a can send you my top gro mdp itp index.ndx files
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Pradip K. Biswas, PhD.
Research Associate, Department of Chemistry;
Cleveland State University, Ohio-44115
Phone: 1-216-875-9723
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