AMBER Archive (2009)

Subject: Re: [AMBER] lipid membrane(dppc) in amber

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Fri May 22 2009 - 08:45:20 CDT

Hi,

On Fri, May 22, 2009 at 4:42 AM, xueqin pang <pangxueqintea_at_yahoo.com.cn>wrote:

> Hello every,
> I am simulating a GPCR in membrane doundaries, using AMBER 9/10. As a
> greenhand of AMBER, I got several problems with the simulation after
> referring to some related papers as well as the manual of AMBER.
> 1. If I am using. GAFF can I use the parameters of GROMOS-96 force field
> for dppc?

First, Mixing force fields is not recommended always.
However, you can try to modify parameters (very carefully) of your force
field. (1-4 scaling--they use different scaling, vdW parameters, etc. )

>
> 2. If not where can I get parameter and topology for dppc in Amber ( I have
> surf the net but field.)

As far as I know, they are not available. You can try to modify a united
atom FF for amber. See J comp chem 20:531-545 (1999).
Voth et al. used DMPC. See Biophys J 93:3470-3479 (2007)

>
> 3. Someone suggested that "doing NPT in AMBER with ntp=2 leads to more
> unrealistic membrane properties than doing NPT in NAMD with the Langevin
> piston method to control the pressure" (
> http://archive.ambermd.org/200808/0100.html). Is that true with you?

No implementation for surface tension in Amber. If the parameterization for
lipids is correct, then you don't have to apply
surface tension to keep the correct area per lipid. However, correct
parameterization is not easy.
One way is that you convert parameter topology file to gromacs form and run
simulations in Gromacs.

HOWEVER, I recommend you just use Namd and Charmm FF (or Gromacs and its FF)
for both protein and lipid.

>
>
> Thanks a lot
>
>
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-- 
Best wishes,

Myunggi Yi
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