Dear AMBER experts
I am trying to learn FEP methodology in AMBER, I have two questions hope you may be able to help me
* In AMBER 10 manual, starting coordinate files must be the same for the two states, perturbed and unperturbed. Accoriding to the input group file:
-O -i mdin -p prmtop.0 -c eq1.x -o md1.o -r md1.x -inf mdinfo
-O -i mdin -p prmtop.1 -c eq1.x -o md1b.o -r md1b.x -inf mdinfob
So, should I equilibrate ONLY one state and use its coordinates to describe the both states?
* In the manual, The implementation requires that the masses of all atoms be the same on all threads. How!!! I see papers studied systems as methanol to methane. Here the masses are not the same.
Any kind of help, would be appreciated.
Thanks in advance;
W. Flak
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Received on Fri Aug 20 2010 - 22:00:03 PDT
