Hi Bill,
It is implemented in tleap (at least in AMBER 11) -- I've used it
myself on several occasions and have output files containing the
conjugate gradient information resulting from the "minimization"
performed by the relax command (as well as the modified coordinate
files showing that it did in fact relax the structure). As you
mention though, relax does have its shortcomings and should not be
used as a substitute for real minimization in sander (or pmemd).
Paul
On Jul 23, 2010, at 9:56 AM, Bill Ross wrote:
>> I just had a quick question: does anyone know if there is a command
>> that can
>> be used with a tleap script to relax a protein system? I know in
>> xleap you
>> can choose "relax selection," I just wasn't sure what the command
>> would be
>> for tleap.
>
> I don't believe this is implemented for tleap.
>
> Note that the relax cmd does not take into account non-bonded
> interactions, so it can lead to atoms passing through each other.
> So 'relax' is best used graphically when selecting a few atoms
> at a time and watching what it does to correct if needed.
>
> Best to use sander to energy minimize a whole protein.
>
> Bill
>
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Received on Fri Jul 23 2010 - 11:00:03 PDT
