Dear Amber users,
I found that the net charge of a POPC molecule is not 0 when Amber lipid
force fields were used.
Could someone give some comments about it?
I am confused because I thought that the net charge of the POPC molecule
should be 0...
Here are brief summary of the net charges of the POPC and the H2O
molecules in my calculation:
POPC with lipid21: 1.86E-07
POPC with lipid14:-1.64E-04
H2O: 0
I calculated the net charge of a molecule by summing up point of charges
(values in "%FLAG CHARGE" section) written in a prmtop file.
I confirmed that the net charge of the H2O molecule was 0, but the net
charge of the POPC molecule was not 0...
In addition, I found that the net charge of the POPC molecule with
lipid14 was much far away from 0 compared with that with lipid21.
The attached files were the prmtop files which I used for the net charge
calculation.
I also have attached PDB and leap input files, which were used to
generate the attached prmtop files.
Please note that the attahced PDB file was generated from an original
PDB file, which consisted of 128 POPC molecules and 5120 H2O molecules.
The original PDB file was prepared with CHARMM-GUI and converted with
charmmlipid2amber.py.
After loading and saving the PDB file in Leap, the information about the
one POPC and the one H2O moleucules were extracted to the attached PDB file.
Sincerely,
Kosuke Tachibana
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Received on Tue Mar 14 2023 - 11:00:02 PDT
