AMBER Archive (2007)

Subject: RE: AMBER: How to decide extra-helical or intra-helical bulge conformation by PTRAJ ?

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Sun Nov 04 2007 - 23:20:48 CST

Dear Sir/Madam,

I am trying to do the umbrella sampling for a dihedral angle, but I want to make sure the rest of the hydrogen bonds remains during the simulations. Are there any way to do so?

I think I cannot forzen or restrained atoms to the cartesian space of page 101 of AMBER 8.0 manual, as the cartesian coordinates were suppose to be change when I change the dihedral angle during the umbrella sampling.

I suspect that I cannot use the distance restraint as listed in the section 5.9 of AMBER 8.0 mannual, as the distances will also store in the DUMPAVE file which is not necessary for the WHAM analysis afterall.

Did I miss any important things here? Please kindly suggest any better way of doing this.

Best regards,

Cat.

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