AMBER Archive (2007)

Subject: AMBER: PMF along 1D axis or every axis

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Fri May 11 2007 - 22:05:57 CDT

Dear Sir/Madam,

I would like to calculate the PMF along the 1D axis, i.e.

                            Receptor ---------> Drug (1D axis is considered
only)

What should I do, distance or angle or torsional restraint during the
umbrella sampling.

On the other hand, if I could like to calculate the PMF along the every
probable axis.

                                                  Drug
                                                    |
                                    Drug <- receptor -> Drug
                                                    |
                                                 Drug

Do I only need to set the distance.restaint only?

Best regards,

Cat

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