[gmx-users] Doubt regarding membrane protein in POPC bilayer
pawan.chinari at gmail.com
Mon Mar 23 14:03:00 CET 2009
Thanks for your help and suggestions.
First I will try to use POPC (the one generated using genconf) . If it
doesnt work then I will switch over to POPE.
I will ask you if I have any further queries.
On Mon, Mar 23, 2009 at 6:26 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Pawan Kumar wrote:
>> Respected Sir,
>> Greetings from Pawan.
>> I read in the manual about the freeze-grps but dint find a good
>> explanation about the usage.
>> Can you please tell me how to use freeze-grps in all dimensions during the
>> minimizations ?
> If you search for "freezegrps" within the list archive (the "Search"
> feature of the Gromacs homepage), you will find several hundred results,
> many of which provide examples of what users are trying and what may or may
> not work. This should be instructive.
> In a general sense, freezegrps are just like anything else under the group
> theory in Gromacs. Make an index group for the group of atoms you want to
> freeze (i.e., headgroups) and the dimensions in which you want them frozen
> (x, y, z - yes(Y) or no(N) for each).
> If you are choosing the route of POPE, it is very difficult to get these
> systems built using InflateGRO. At least, that has been my experience.
> Prepare to spend a lot of time with trial and error and very careful
> Thanking you,
>> On Mon, Mar 23, 2009 at 5:58 PM, Justin A. Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu>> wrote:
>> Pawan Kumar wrote:
>> Respected Sir,
>> Thanks for all your help, suggestions and guidance.
>> I have few more queries.
>> Which type of box is appropriate in editconf - cubic or triclinic ?
>> That depends entirely upon the dimensions of your system and what is
>> adequate to accommodate the size of your embedded protein.
>> I have read in one of your mails in the archives that POPE
>> bilayer contains some bad interactions. As it contains more no.
>> of lipids (340) it covers the full protein ( trimer which I am
>> working on ) other than the few loop regions. How far that
>> bilayer can be used or is it fine to use the biger bilayer of
>> popc128a whcih I obtained by genconf ?
>> The choice of lipid should not be based on a size convenience. It
>> should be based on a valid model system, and experimental evidence
>> to which you can correlate your results, if possible.
>> POPE presented a terrible challenge, since during the in vacuo
>> InflateGRO minimizations, the headgroups folded in on themselves to
>> form intra-molecule hydrogen bonds that resulted in a collapse of
>> the molecule. The solution was to use freeze-grps in all dimensions
>> during these minimizations, and then equilibrate very carefully.
>> Justin A. Lemkul
>> Graduate Research Assistant
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
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