thanks for the files.
1) you should not use TIP3P with the ff19SB force field. TIP3P is (in my
opinion) old and outdated, and we have much better models now (such as
OPC). Even for a 3-point model, there are better options.
https://ambermd.org/AmberModels_proteins.php
2) try to source the leaprc file for the water instead of loading a frcmod
like you have in your input. for examples, see
https://ambermd.org/AmberModels_ions.php. In your case, use "source
leaprc.water.opc"
On Thu, May 9, 2024 at 4:28 PM Xylia Peters <xyliapeters.yahoo.com> wrote:
> Dear Carlos,
>
> I trust you are well.
>
> I apologize.
>
> Please find attached my tleap.pdb file and my tleap.all file. I've also
> included the error, output, and log file for tleap just in case these would
> help.
>
> Kind regards,
> Xylia
>
> On Thursday, May 9, 2024 at 10:01:49 PM GMT+2, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 09 2024 - 14:00:02 PDT
