source leaprc.protein.ff14SB
set default PBRadii mbondi3
source leaprc.water.tip3p
source leaprc.gaff2
# Loading parameters for staple molecule
loadamberparams link.frcmod
# Loading chain A with staple coordinates
recAL = loadpdb recal.pdb
# Loading the rest of the protein complex
recb = loadpdb rec_rest.pdb
LIG = loadmol2 link.mol2
# Save the parameters and restart file
saveamberparm recAL gfp.parm7 gfp.rst7
# Quit the LEaP session
quit
On Wed, Jan 8, 2025 at 3:03 PM Airy Sanjeev <airy.sanjeev01.gmail.com>
wrote:
> Hello Amber users,
>
> I have a protein that is covalently attached to two ligands at two
> positions 272 and 276, and these ligands are covalently attached to each
> other. I am not able to save the parameter and coordinate files. I am
> attaching the files here. Any lead would be much appreciated.
>
> --
> Regards
>
> Airy
>
>
>
--
Regards
Airy Sanjeev
Post-Doctoral Fellow
IFM Bioinformatics Division
Campus Valla, Physics Building, D301, Linköping University
Linköping, Sweden
Phn: +46-727454874
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Received on Wed Jan 08 2025 - 06:30:03 PST
