AMBER Archive (2006)

Subject: Re: AMBER: PMEMD with NMR restraint and position restraint

From: Robert Duke (
Date: Mon Jul 17 2006 - 22:03:29 CDT

Ting -
Exactly what does your input mdin file look like? I believe pmemd takes a subset of the possibilities for specifying both nmr and positional restraints; I have not tried to fix this code to accept all possibilities because the exact definition of "all possibilities" has been a poorly specified moving target. Anyway, if you show us exactly what you did, we can probably propose alternatives that work (folks that do this routinely, please jump in; I don't have a good test case myself).
Regards - Bob Duke
  ----- Original Message -----
  From: Ting Wang
  Sent: Monday, July 17, 2006 7:18 PM
  Subject: AMBER: PMEMD with NMR restraint and position restraint


  I am running PMEMD/amber9. I need to set both NMR distance restraints (nmropt=1) and position resstraints (ntr=1). But I found PMEMD can work with either restraint type alone but not both together.

  Any suggestion?



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