AMBER Archive (2008)

Subject: RE: AMBER: Not integral charge increasing with number of lipids

From: Ross Walker (
Date: Thu Aug 07 2008 - 10:24:28 CDT

Hi Rebeca,

Following up on the previous email.

> I would like to simulate a big DOPC membrane and I have built the files
> dopc.prepin and dopc.frcmod using the Antechamber program.
> With a small membrane, everything is OK (the total charge is zero, as it
> was

I'm not sure I'd trust Antechamber and GAFF to work properly with lipids. If
you do want to use it here make sure you test things like area per lipid,
surface tension etc. I would also do a proper charge fit rather than just
using AM1/BCC - especially since last time I checked antechamber didn't
enforce the constraints on methyl and methylene hydrogens correctly. Note
these is a DOPC force field in the contributed parameters section (see the
amber website for the link) - however I haven't looked at what was done
here, they may have used GAFF as well. Ideally you probably want to use
something like the CHARMM lipid force field although this may not be trivial
to use in AMBER.

> expected), but when the number of lipids increase (for example, with 500
> lipids) the charge of the membrane becomes a not integral (for example,
> with
> 500 lipids the charge is -0.015000.

You need to manually adjust your DOPC prep file so that the charges sum
exactly to zero, as it is right now you have rounding differences between
the QM calculation and the prep file (or possibly from the prep file to
leap) that means it doesn't sum exactly to zero. Adjust each atom to round
it manually to 3 decimal places and then adjust things so all the 3 d.p.
numbers add up to zero.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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