Is residue PCA the one that is in your ligand library ?
You might want to consume usual troubleshooting steps, like attempting to
build the ligand alone before trying a complex.
On Mon, Apr 15, 2024, 7:17 PM ABDELATIF MESSAOUDI via AMBER <
amber.ambermd.org> wrote:
> Dear AMBER users,
>
> I am using PDB file (code pdb :4w93) structure for molecular dynamics
> simulation with AMBER22.
>
>
> First I ran the command:
>
>
> - antechamber -i Lig.log -fi gout -o Lig.mol2 -fo mol2 -c resp
>
> - parmchk -i Lig.mol2 -o Lig.frcmod -f mol2
>
> after # xleap
>
> - source leaprc.gaff2
>
> - source leaprc.protein.ff14SB
>
> - source leaprc.water.tip3p
>
> - loadamberparams Lig,frcmod
>
> - MOL=loadmol2 Lig,mol2
>
> - a=loadpdb 4w93,pdb
>
> - check a
>
> saveamberparm a Lig.top Lig.crd
>
> quit
>
> But at the last step, the parameters cannot be saved because of this kind
> of errors:
> [image: image.png]
>
> How can this problem be solved?
> Thank you for your help.
>
> Abdelatif
> University of Batna
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Received on Mon Apr 15 2024 - 18:00:02 PDT
