Hi Kosuke,
I think this has come up on the mailing list once before - the POPC charges were derived from averaging of RESP fits, so the very slight non-zero charge you see is round-off error. However, when you simulate with PMEMD, this will not be an issue since the code will force neutrality of the box.
Best,
Callum
-----Original Message-----
From: Kosuke Tachibana via AMBER <amber.ambermd.org>
Sent: Monday, March 13, 2023 1:28 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Net charge of a POPC molecule is not zero
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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
https://urldefense.com/v3/__http://charmmlipid2amber.py__;!!N3hqHg43uw!tXejgNsggLJd5dW31F9mwlt6ZHSH1sKtD4yAZVgswTS7u4IuFiuiqeIox7M531IrjLPVRNRf_nXyTJlIx6sy$ .
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 Wed Mar 15 2023 - 07:30:05 PDT
