the format in which your input is included makes it very difficult to read.
I suggest attaching the original as a file, or making sure the input is
given line by line, copied exactly from the real input file, with each
command on a separate line.
On Thu, May 9, 2024 at 1:08 PM Xylia Peters via AMBER <amber.ambermd.org>
wrote:
> 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 - 13:30:02 PDT
