Hi Sunita,
I guess this error is because you have Mg2+ ions with residue name as “Mg” and atom name as “Mg2” in your PDB file, which has nothing to do with the Mg2+ atom type.
Please read this webpage for how LEaP recognizes atomic ions: https://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.htm <https://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.htm>.
In order to make LEaP to recognize the Mg2+ ions, I suggest you to treat all the Mg2+ ions with residue name as “MG” and atom name as “MG” in your PDB file.
Hope it helps,
Pengfei
> On Mar 25, 2020, at 10:15 AM, Sunita Patel <sunita.patel.cbs.ac.in> wrote:
>
> Dear Amber Users,
>
> I am generating the coordinate and topology files. My initial structure is
> a protein bound to DNA and two Mg2+ ions. When I am running tleap I am
> getting the error Mg2 does not have a type. I checked the
> "leaprc.water.tip3p" file which shows atom type of Mg2+. Then, why am I
> getting this error.
>
> I am stuck because of this problem.
> Your help will be highly appreciated.
>
> Sincerely,
> Sunita
>
> -------------------------------------------------------
> /home/external/cbs/sunitap/softwares/amber18/bin/teLeap: Warning!
> -no luck
> Added missing heavy atom: .R<CGLN 123>.A<OXT 18>
> Creating new UNIT for residue: Mg sequence: 148
> Created a new atom named: Mg2 within residue: .R<Mg 148>
> Creating new UNIT for residue: Mg sequence: 149
> Created a new atom named: Mg2 within residue: .R<Mg 149>
> total atoms in file: 1249
> Leap added 1030 missing atoms according to residue templates:
> 1 Heavy
> 1029 H / lone pairs
> The file contained 2 atoms not in residue templates
> Checking Unit.
>
> /home/external/cbs/sunitap/softwares/amber18/bin/teLeap: Warning!
> The unperturbed charge of the unit (-22.000000) is not zero.
> FATAL: Atom .R<Mg 148>.A<Mg2 1> does not have a type.
> FATAL: Atom .R<Mg 149>.A<Mg2 1> does not have a type.
>
> /home/external/cbs/sunitap/softwares/amber18/bin/teLeap: Fatal Error!
> Failed to generate parameters
>
> Exiting LEaP: Errors = 1; Warnings = 5; Notes = 1.
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Received on Thu Apr 09 2020 - 09:30:02 PDT
