On Mon, Jun 08, 2020, anirudh mantri wrote:
>
>We are trying to construct an Au-S-(CH2)6-SH system topology file in Amber.
>We used Chem3D pro to make a mol2 file. We are trying to use this mol2 file
>to generate the topology files using antechamber. While following the
>antechamber tutorial, I was using the Parmchk to generate the frcmod file
>to generate missing parameters.
Are there any missing parameters (beside those involving Au, which you
say you have anyway)? It seems possible that you might just be able to
skip the parmchk2 step entirely.
If tleap still finds missing parameters, you might try parmchk2 with a
structure that just replaces Au with H.
...dac
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Received on Mon Jun 08 2020 - 07:00:02 PDT
