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 Wed Mar 25 2020 - 07:30:02 PDT
