On Sun, Mar 29, 2020, Rosellen, Martin wrote:
>
>I want to solvate a structure (5rft) containing small ligands. I download
>the pdbs of the ligands and convert them into a mol2 file. In tleap
>checking the loaded pdb I get a lot of errors of this type:
>
>Error: Could not find angle parameter: ca - ca - ca
>Error: Could not find angle parameter: ca - ca - ha
It looks like you failed to load gaff2.dat, which contains the
parameters you need.
>
>I tried to use parmchk2 to create frcmod files but get a Segmentation fault after warnings of this kind:
>
>Warning: Atom type (C.ar) is not in PARMCHK.DAT; using default values
> for improper_flag [0], group_id [0], and equivalent_flag [0].
Looks like you created your mol2 with some other program(?) that is
using Sybyl atom types. parmchk2 can only handle Amber or gaff(2) atom
types. You should use antechamber to make the mol2 files (with gaff2
atom types).
....good luck...dac
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Received on Sun Mar 29 2020 - 08:00:03 PDT
