AMBER Archive (2006)

Subject: Re: AMBER: MD with restraint (nmropt=1)

From: David A. Case (case_at_scripps.edu)
Date: Tue Dec 05 2006 - 15:24:37 CST

On Tue, Dec 05, 2006, a a wrote:
>
> I could like to run a minization and MD calculation with six hydrogen bond
> restrainted. they are
>
> (residue 4, atomname H61)........(residue 1, atomname O4)
> (residue 4, atomname N1)...........(residue 1, atomname H3)
> (residue 4, atomname H2)...........(residue 1, atomname O2)
> (residue 3, atomname H41).........(rsidue 2, atomname O6)
> (residue 3, atomname N3)...........(residue 2, atomname H1)
> (residue 3, atomname O2)............(residue 2, atomname H21)

Each restraint needs to be in its own &rst namelist. Also note that atom names
are case sensitive, "h3" is not the same as "H3".

....dac

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