AMBER Archive (2006)

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

From: Ting Wang (
Date: Tue Jul 18 2006 - 15:12:41 CDT

Hi Bob,

Here is my input file, I also tried to put the nmr restraint part after the
positional restraint part.

Thank you very much!


> 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
> To:
> Sent: Monday, July 17, 2006 7:18 PM
> Subject: AMBER: PMEMD with NMR restraint and position restraint
> Hi,
> 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?
> Thanks,
> Ting

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