On 2011-12-12, at 6:49 AM, Daniel Sindhikara wrote:
> Hi,
> Two issues tripped me up recently with regards to MDL format. I wonder if
> we could clarify them in the AMBER manual.
> First:
> The "CHG" Flag says:
>
> %FLAG CHG
> %FORMAT(5e16.8)
>
> REAL*8(NSITE) Partial charge for each solvent site (e).
> But I believe it has to be multiplied by 18.2223.
>
Thanks for catching this oversight. The manual for the next release will clarify this point.
> Also,
>
> %FLAG LJSIGMA
>
> %FORMAT(5e16.8)
>
> REAL*8(NSITE) Lennard-Jones rmin/2(σ ∗/2) for each solvent site (Å). Note
> that this is not σ .
> Can we rename this variable? Maybe LJRMIN. You could see how this could
> cause problems.
>
Yes, this is a known issue and addressed in the manual. I agree that the wording is not as clear as it should be and have updated the description. A new version of this file format will be released in the future to address this unfortunate misnaming and add some flexibility.
Thank you for your input,
Tyler
________________________________________________________________
Tyler Luchko
Postdoctoral Associate
Case Group
BioMaPS Institute
Rutgers University
Piscataway, New Jersey
tluchko.rutgers.edu
732-445-0334
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Received on Tue Dec 13 2011 - 14:30:03 PST
