Re: [AMBER] tleap for Mg2+ data type

From: Sunita Patel <sunita.patel.cbs.ac.in>
Date: Fri, 10 Apr 2020 08:09:05 +0530

Hi Pengfei,

Thank you so much.
That problem is already solved.

Sincerely,
Sunita


On Thu, Apr 9, 2020 at 9:50 PM Pengfei Li <ambermailpengfei.gmail.com>
wrote:

> 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 - 20:00:02 PDT
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