Dear Amber developpers,
We are trying to perform MD simulations using AMBER11 on a system
containing a protein, a cofactor, a substrate, and solvent molecules. Our
system contains 69 different atom types.
Sander immediately stopped with an error because nttyp (defined as
ntypes*(ntypes+1)/2 ) exceeds the limit of 1830. However, the maximum
number of atom types (max_atom_types) is set to 100, which would lead to a
maximum value for nttyp of 5050. So we changed the maximum value of nttyp
to 5050=100*101/2 in the rdparm.f routine.
With this patch, sander runs, but leads to huge 1,4-VDW energies (the
prmtop file was generated with chamber from a charmm force field, and we
checked that the procedure works fine on subsystems with fewer than 60
atom types). Those 1,4 energy terms are 10000 times higher than the same
terms calculated with NAMD. All other energies seem to be correct. We
tried to minimize only parts of the system, and as soon as our subsystem
contains less than 60 atoms everything is fine, but each time there are
more than 60 atom types this 1,4-VDW energy gets enormous.
Could you please tell us if this abnormal behaviour of the 1,4-VDW
energies could actually be related to the number of atom types which is
too large ? What else (in addition to the upper bound of nttyp in
rdparm.f) should we change to be able to work with more than 60 atom types
?
Thank you very much for your help.
Best regards,
Elise Duboué-Dijon,
PhD Candidate
Ecole Normale Supérieure, Paris, France
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Received on Thu Nov 22 2012 - 01:00:02 PST
