Hi Vlad:
thanks a lot for kind messages.
How about Gromacs or Desmond? Is NAMD the only tool that good for
surface tension ?
THX
On 12/21/2011 07:37 AM, Vlad Cojocaru wrote:
> Dear Albert,
>
> If you follow previous threads regarding lipid simulations with Amber ff, you'll realize that some studies are done with the Gaff parameters available in the literature
>
> However, as the gaff parameters have the problem of getting a gel-phase bilayer in pure npt sim, you'd need to run the simulations with namd and apply a surface tension.
>
> Alternatively, you can use glycam for lipids as well. However same problem as with gaff and besides glycam uses a different 1-4 scaling factor than amber, so another level of complication.
>
> To my knowledge, the only atomistic force field for lipids that reproduces nicely lipid properties in pure npt sims is the newest charmm ff.
>
> The gaff parameters need some attention for further development to achieve stable npt simulations with lipids
>
> Regards,
> Vlad
> ---
> Dr. Vlad Cojocaru
>
> MPI Muenster
> Roentgenstrasse 20
> 48149 Muenster
> Germany
> Tel: +49-251-70365324
>
> *** Sent from my Sony XPERIA ARC
> *** Sorry for being short
> *** Sorry for any errors
>
> Albert<mailmd2011.gmail.com> wrote:
>
> GPCR simulation is a very hot topic nowadays. It is worth Amber
> developer to do something towards this purpose.
>
> I strongly suggest that the developer can consider the membrane system
> builder, lipids forcefiled, relaxation protocol, ligand topology tools
> during development. At least, cooperating with Desmond is also a good
> choice since the system builder, lipids forcefiled and relaxation
> protocol is good in Desmond. The only stuff is ligand topology and Amber
> got such kind of tools to complement it.
>
>
>
> On 12/21/2011 01:07 AM, Aron Broom wrote:
>> Yes, there is no reason why you can't do a simulation with a protein in a
>> membrane in AMBER. I'm not aware of any tutorials on this topic, but there
>> are some web services where you can get the coordinate files for
>> pre-equilibrated membranes, this might be a good place to start.
>>
>> On Tue, Dec 20, 2011 at 7:03 PM, Carlos Simmerling<
>> carlos.simmerling.gmail.com> wrote:
>>
>>> I'm not sure it's that simple- in principle, Amber can do membrane
>>> simulations and examples have been published. If one is thinking of a
>>> particular simulation method that is wanted to enforce aspects of membrane
>>> structure and perhaps stop the inaccurate force fields from doing bad
>>> things, then it's a different question than just whether Amber can actually
>>> run membrane simulations...
>>>
>>> On Tue, Dec 20, 2011 at 6:54 PM, Albert<mailmd2011.gmail.com> wrote:
>>>
>>>> As far as I know, Amber doesn't support membrane protein simulation. It
>>>> is said that the next version of Amber may update this function.
>>>>
>>>>
>>>>
>>>> On 12/20/2011 04:56 PM, Rajesh Singh wrote:
>>>>> Dear All,
>>>>>
>>>>> I am facing problems in performing MD of membrane proteins (GPCRs). I
>>>> would
>>>>> highly appreciate if anybody can provide me a tutorial for performing
>>>>> membrane dynamics using AMBER.
>>>>>
>>>>> Thanks and regards
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Received on Wed Dec 21 2011 - 00:00:02 PST
