On Fri, Apr 23, 2021, Swisher, Justin S wrote:
>
>It's me again! So, this email is more of a conceptual issue I'm having with
>both dealing with a forcefield (in this instance the GAFF) and trying to
>get X-Leap to recognize the individual units I'm trying to stitch together
>with T-Leap.
>
>These issues I think are tied together. I found a tutorial that I thought
>was getting me to my goal where I was inputting atom types with the
>gaff atom type style into the molecule table in X-Leap ...
Although it is possible to fill in the table in xleap, that is not a route
any user is expected to travel. The recommended path is this: build the
library files (in .prepi or .mol2 format) using antechamber, and the frcmod
files using parmchk2. Then stich them together with tleap. Avoid using
xleap at all.
Second point: generally, one wants to input the starting structure of the
entire system into a single PDB file. (Amber is not particularly good at
doing this task, so one often uses other software.) Then, in tleap, load
all of the UNITs (residues), then use loadPdb to load in the complete pdb
file. Once that is working, you are ready to save the prmtop/inpcrd files,
and continue.
....hope this helps....dac
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Received on Fri Apr 23 2021 - 18:30:02 PDT
