AMBER: QMMM question

From: xiaoqin huang <>
Date: Fri, 07 Oct 2005 00:09:53 -0400

Dear amber users, I have a question on QMMM with Amber8.
I want to do the umbrella sampling for the reaction: CL (ion, -1e) +
CH3CL-----CLCH3 + CL(ion, -1e), and calculate the potential of mean force
(PMF) of this reaction, I solvatecap the solute (the whole reactants, CL
+CH3CL) at 18A size, and add one counterion (Na+) to balance the charge of
whole system. All reactant atoms (totally 6, not include the Na+) are
treated by QM, while all others are as MM.
I starte relaxing the system for 5000 steps, and it run smoothly over and
get the restart file (input file is attached)
Next, I want to do the MD for the whole system, I use the NMR constraints
for the reaction coordiamtes sampling, the restraint file is dist.RST.
however, after the input file is read (attached is the input
file), it stopped with a fatal error as:
Number of triangulated 3-point waters found: 724
Link atoms MUST be optimized before MD run

by the way, I have the (assign the charge of QM part of -1e) under
the subdirectory where the job is submitted.

I have compiled the amber8 in serial, and patch the bugfix.all, but get some
rejects (attached file rjects).

is there anyone could help me find what is wrong, whether the input file or
something else?

I attached the input files both for minimization and MD, please have a look.

thanks very much!

xiaoqin huang

college of pharmacy
university of kentucky

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Received on Fri Oct 07 2005 - 05:53:01 PDT
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