On Tue, Dec 20, 2011 at 7:21 PM, Albert <mailmd2011.gmail.com> wrote:
> of course if we do something, each of us hope it should be something
> reliable not just can or can not.... I also looking forward the update
> function for membrane protein in Amber. In fact, most people would like
> to use CHARMM36 for membrane system and the problem for many tools is
> the topology file for ligand. Probably, Amber developer should also
> consider how to solve this problem. Since amber get Antechamber tool for
> ligand building, probably someone should provide how to build CHARMM FF
> based topology for ligand.
>
There is. It's called chamber ;). It will take a CHARMM PSF file and
translate it into an Amber topology and inpcrd file suitable for running in
sander and pmemd.
Like Carlos (and others) have mentioned already, there's no reason that
Amber can't be used for membrane simulations. There are techniques
commonly applied to membrane simulations that Amber 11 does not have,
though, such as constant surface tension and other weird constant pressure
techniques (non-isotropic, semi-isotropic, etc.). They should be
up-and-coming for Amber 12, though.
I believe an Amber lipid force field is receiving active attention from
Amber developers, but since I'm not one of them I can't comment any further.
It is said that GAFF is also good enough for lipids simulation and some
> paper was already published based on this. However, what I found is that
> most people would like to use POPC lipids. But someone else prefer POPE
> or else. Probably, Amber developer can also consider merge the POPC,POPE
> parameters into the latest Amber99SB FF which can make the case much
> more convenient.
>
FF99SB (which is the protein part of ff10) is just a protein force field.
The rest of the underlying force field there is ff99, and there are a
number of better alternatives for systems that are not proteins (like
ff99bsc0 for nucleic acids, which is included, and expanded upon, in ff10).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Dec 20 2011 - 20:30:03 PST
