Re: [AMBER] VMD lipid in AMBER

From: Benjamin Madej <>
Date: Fri, 31 Jan 2014 12:27:44 -0800

Hi Rejwan,

What version of VMD did you build your structure with? I assume you're
trying to use the Lipid11 force field? What version of Amber are you using
and what commands do you use to load your structure? Can you give any
output from charmmlipid2amber.x and LEaP?

Without that information, we won't be able to help.

If there's something going on with the charmmlipid2amber.x script, can you
send me your POPC pdb off the mailing list and I can take a look at it.

All the best,
Ben Madej
Walker Molecular Dynamics Lab

On Fri, Jan 31, 2014 at 11:40 AM, Rejwan <> wrote:

> I am having issue in converting VMD made POPC bi-layer into LEAP
> compatible lipid. The charmm2amber script seems to have some mixed up of
> atoms in PC, PL and OL residues. That means some of OL residues got PC
> atoms or so. Also LEAP complains of C12 atom in OL residue and so.
> Is there any way to clean them up so that can be imported into LEAP.
> Thanks.
> Rejwan Ali
> PS: In earlier mail there is no subject. So please ignore it.
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Received on Fri Jan 31 2014 - 12:30:02 PST
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