Dear Amber users,
It worked.
Thank you Stephan. One more query.
The "TER" statement is provided to separate the disconnected segments.
Do I need to provide TER statement to separate two Mg2+ ions?
This is the end part of my PDB file. Is it fine or I need another TER
statement between two Mg2+ ions?
-------------------------------------------------
ATOM 485 OP1 DG3 147 -9.954 -7.989 10.887 1.00 0.00
O
ATOM 486 OP2 DG3 147 -8.081 -8.158 12.615 1.00 0.00
O
TER
HETATM 487 MG MG 148 -12.766 -5.036 -6.481 1.00 0.00
Mg
HETATM 488 MG MG 149 -10.500 9.645 5.380 1.00 0.00
Mg
END
--------------------------------------
Thank you so much for your help.
Sincerely,
Sunita
On Wed, Mar 25, 2020 at 8:08 PM Stephan Schott <schottve.hhu.de> wrote:
> Hi Sunita,
> I believe this is because the residue name to be used by LEaP is defined in
> atomic_ions.lib. Try changing Mg2+ for MG, and let us know if that works.
> Cheers,
>
> El mié., 25 mar. 2020 a las 15:13, Sunita Patel (<sunita.patel.cbs.ac.in>)
> escribió:
>
> > 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Stephan Schott Verdugo
> Biochemist
>
> Heinrich-Heine-Universitaet Duesseldorf
> Institut fuer Pharm. und Med. Chemie
> Universitaetsstr. 1
> 40225 Duesseldorf
> Germany
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Received on Wed Mar 25 2020 - 17:30:02 PDT
