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leelasd / ligpargen

A repository for tutorials and FAQ's about LigParGen
http://traken.chem.yale.edu/ligpargen/
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LigParGen Parameterized Ligand Introduces Non-zero Charge to The System #59

Open MikeBie opened 4 years ago

MikeBie commented 4 years ago

Issue Information

Software name & Version : Gromacs-2020.2 Method: oplsaam.ff forefield; command: gmx grompp -f ions.mdp -c input.gro -p topol.top -o ions.tpr Note: _NOTE 2 [file topol.top, line 55]: System has non-zero total charge: -7.999600 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer_

This leads later to a "fatal error" in a energy minimization job after neutralizing the system with ion because there is + 0.0004 total charge. I can overwrite this and the minimization succeeds. I'm just wondering if this is an indication of poor paramatization of the ligand. Any thoughts?

qqlovekerry commented 3 years ago

Hello, I also encountered this problem. I uploaded the molecule to the webserver. The total charge of the atoms in the generated .itp file is +0.0007. It seems to be a very small number but not zero. Could the exports or developers please help with this problem? How can we make the total charge to be zero?