Good day,
I trust you are well.
I am currently experiencing issues with tleap and hope you would be able to assist me.
I am currently conducting protein-protein docking and running the initial phase- tleap. However, I am unable to get through the charge phase as I keep generating an error in my output file as follows:
Converting C-terminal residue name to PDB format: CHIE -> HIEUsing H(N)-modified Bondi radiiTotal unperturbed charge: -5.000000Total perturbed charge: -5.000000
/apps/chpc/chem/amber/18/bin/teLeap: Fatal Error!addIons: Argument #2 is type String must be of type: [unit]
addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_Adds counterions in a shell around _unit_ using a Coulombic potentialon a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must beopposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,the specified numbers of _ion1_ [_ion2_] are added [in alternating order].If solvent is present, it is ignored in the charge and steric calculations,and if an ion has a steric conflict with a solvent molecule, the ion ismoved to the center of said molecule, and the latter is deleted. (Toavoid this behavior, either solvate _after_ addIons, or use addIons2.)Ions must be monoatomic. Note that the one-at-a-time procedure is notguaranteed to globally minimize the electrostatic energy. When neutralizingregular-backbone nucleic acids, the first cations will generally be addedbetween phosphates, leaving the final two ions to be placed somewhere aroundthe middle of the molecule.The default grid resolution is 1 Angstrom, extending from an inner radiusof (max ion size + max solute atom size) to an outer radius 4 Angstromsbeyond. A distance-dependent dielectric is used for speed.
I have searched the internet and have not found a resolution. My current input file looks as follows:
source leaprc.protein.ff19SBsource leaprc.gaff2
loadamberparams frcmod.ionsjc_tip3preceptor1 = loadPDB rec1.pdbreceptor2 = loadPDB rec2.pdbsaveAmberParm receptor1 rec1.top rec1.crdsaveAmberParm receptor2 rec2.top rec2.crdcomplex = combine {receptor1 receptor2}saveAmberParm complex com.top com.crdsavepdb complex complex_gas.pdbset default PBRadii mbondi2charge complexaddIons2 complex Na+ 0addIons2 complex Cl- 0solvateBox complex TIP3PBOX 12.0saveAmberParm complex com_solvated.top com_solvated.crdsavepdb complex com_solvated.pdbquit
Please could you assist? Your feedback is appreciated.
Kind regards,Xylia
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Received on Thu May 09 2024 - 10:30:02 PDT
