On Sat, May 29, 2021, Rana Rehan Khalid wrote:
>Creating new UNIT for residue: LIG sequence: 235
>Created a new atom named: N1 within residue: .R<LIG 235>
>Created a new atom named: Cl1 within residue: .R<LIG 235>
>Created a new atom named: C2 within residue: .R<LIG 235>
>
>"source leaprc.protein.ff19SB",
> "source leaprc.gaff",
> "source leaprc.water.tip3p",
> "loadamberparams dummy.frcmod",
> "loadamberparams LIG1.frcmod",
> "lig = loadmol2 LIG.mol2",
This looks suspicious: should the unit not be capitalized? Try changing lig ->
LIG.
> "DM1 = loadmol2 dm1.mol2",
> "DM2 = loadmol2 dm2.mol2",
> "DM3 = loadmol2 dm3.mol2",
Add a "list" command here, and see what units are loaded.
> "model = loadpdb aligned_with_dummy.pdb", ERROR COMES HERE WHEN I
>LOAD DUMMY
....dac
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Received on Sun May 30 2021 - 18:00:02 PDT
