Dear Dr. Dickson,
Thank you for the response, and I am sorry that I seem to have missed
the previous post on the mailing list.
By multiplying the atomic charges written in the lipid21.lib file by a
constant of 18.2223, I confirmed that the slight non-zero charge of the
POPC molecule was caused by round-off error.
I also confirmed that PMEMD neutralized the box in the mdout file.
Thank you very much for your kind help.
Sincerely,
Kosuke Tachibana
On 2023/03/15 23:22, Dickson, Callum wrote:
> 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
>
> This Message is from an External Sender. Do not click links or open attachments unless you trust the sender.
>
> 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 Sat Mar 18 2023 - 02:00:03 PDT
