From: Bala subramanian (bala.biophysics_at_gmail.com)
Date: Mon Jul 28 2014 - 12:46:39 CDT
Hi,
1) It was by mistake i wrote 2b7 instead of charmm27.
2) The experimental work indicates no implication on the time scale of the
conformational changes.
On Mon, Jul 28, 2014 at 7:40 PM, Kenno Vanommeslaeghe <
kvanomme_at_rx.umaryland.edu> wrote:
> (1) There is no CHARMM 2b7. The previous _CGenFF_ release was 2b7, but
> CGenFF cannot/should not be used for biomolecules. As for the biomolecular
> force field, there is:
> * the CHARMM22 protein parameter set (~1992).
> * the CHARMM27 lipid parameter set (~2000).
> * the CHARMM22/CMAP protein parameter set (~2003), which was often
> used together with CHARMM27. Although obsolete, this combination still
> appears to be popular with VMD and NAMD users.
> * the CHARMM36 force field (~2012), which covers all classes of
> molecules (including proteins and lipids) and has a number of important
> improvements that may be relevant to your problem.
>
> (2) Just checking; does experiment indicate it takes only 60ns at room
> temperature for the pore to open up to 10A ?
>
>
>
>
> On 07/28/2014 01:08 PM, Bala subramanian wrote:
>
>> I missed to indicate the simulation time in the previous mail. We
>> simulated upto 60ns.
>>
>>
>> On Mon, Jul 28, 2014 at 7:06 PM, Bala subramanian
>> <bala.biophysics_at_gmail.com <mailto:bala.biophysics_at_gmail.com>> wrote:
>>
>> Hi,
>> We have used charmm 2b7 ff for the assembly, we simulated it in NVT
>> ensemble with electric field applied to see ionic passage.
>>
>> The experimental evidence suggest a pore opening of up to 10A while we
>> have ~2 Ang opening. The observations are based on pore dimension
>> estimations.
>>
>>
>>
>>
>> On Mon, Jul 28, 2014 at 5:57 PM, Kenno Vanommeslaeghe
>> <kvanomme_at_rx.umaryland.edu <mailto:kvanomme_at_rx.umaryland.edu>> wrote:
>>
>> What force field are you using? How long did you simulate? How did
>> you quantify "conformational changes"? How different is it from
>> "experiment"?
>>
>> On 07/28/2014 11:19 AM, Bala subramanian wrote:
>>
>> Friends,
>>
>> I am new to membrane protein simulations. We have simulated a
>> protein in a
>> DOPC bilayer at 303K and we found that the level of protein
>> conformational
>> changes is not similar to what has been observed in
>> experiments. My PI
>> suggested to try higher temperature like 320K to see if we are
>> able to see
>> larger changes in the conformation.
>>
>> I am looking fwd to hear from any of you with experience in
>> memb-prot
>> simulation if such high temperature can be attempted with DOPC
>> bilayer.
>> Any information on some relevant literature would be of great
>> help.
>>
>> Thank You,
>> Bala
>>
>> --
>> C. Balasubramanian
>>
>>
>>
>>
>>
>> --
>> C. Balasubramanian
>>
>>
>>
>>
>> --
>> C. Balasubramanian
>>
>
>
-- C. Balasubramanian
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