Well, pmemd varies on this in being consistent with the current manual :-).
You can't do alignment and chem shift restraints in pmemd, and it depends on
picking up your attempt to do this by the nmropt=2. So beware (this stuff
IS documented as not being done by pmemd).
Regards - Bob Duke
----- Original Message -----
From: "David A. Case" <case.scripps.edu>
To: <amber.scripps.edu>
Sent: Wednesday, February 16, 2005 4:53 PM
Subject: Re: AMBER: Amber7 nmropt
> On Wed, Feb 16, 2005, Markus W. Germann wrote:
>
>> By accident, I left nmropt=1 for an Amber 7 run, subsequently I rerun
>> this with nmropt=2 (as per manual)
>> The data from both runs are identical and both contain alignment
>> restraints.
>
> The alignment and chemical shift restraints are always included, as long
> as the correponsding restraint files have been defined. See lines
> 482-484 of force.f (in Amber 7). Hence, alignment constraints are not
> influenced by the value of nmropt (as you found).
>
> This is consistent with the description in Section 5.12 of the manual,
> but is not quite consistent with the description of the "nmropt" variable.
>
> I'll make a note to update the manual. Thanks for the report.
>
> ...dac
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Received on Wed Feb 16 2005 - 23:53:00 PST
