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
LOAD DUMMY
"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"
Best
Rehan
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Received on Sat May 29 2021 - 15:00:02 PDT
