[AMBER] Umbrella sampling (Protein Receptor--ligand)

From: Rana Rehan Khalid <ray.binm.gmail.com>
Date: Sat, 29 May 2021 17:44:39 -0400

Dear Amber User

In umbrella sampling at the stage of """"put all together"""
I am facing error kindly guide where I am wrong

At the end of """"add dummy atom stage *aligned_with_dummy.pdb* generated

structure.save("complex/aligned_with_dummy.pdb", overwrite=True)

When I loading this aligned_with_dummy.pdb at put it all together stage lit
gives me error

Warning: -no luck
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>

However I prepared this LIG Mol2 and frcmod files through ANTECHEMBER. I
use there commands for parameterization of LIG

antechamber -fi pdb -fo mol2 -i LIG.pdb -o LIG1.mol2 -c bcc -pf y -nc 0
parmchk2 -i LIG1.mol2 -o LIG1.frcmod -f mol2

Here is the tleap script I use in put all together stage

"source leaprc.protein.ff19SB",
    "source leaprc.gaff",
    "source leaprc.water.tip3p",
    "loadamberparams dummy.frcmod",
    "loadamberparams LIG1.frcmod",
    "lig = loadmol2 LIG.mol2",
    "DM1 = loadmol2 dm1.mol2",
    "DM2 = loadmol2 dm2.mol2",
    "DM3 = loadmol2 dm3.mol2",
    "model = loadpdb aligned_with_dummy.pdb", ERROR COMES HERE WHEN I
    "solvatebox model TIP3PBOX 10.0",
    "addions model Cl- 0",
    "addions model Na+ 0",
    "check model",
    "savepdb model complex-dum.pdb",
    "saveamberparm model complex-dum.prmtop complex-dum.rst7"

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Received on Sat May 29 2021 - 15:00:02 PDT
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