[gmx-users] Re: Justin lipid-position restraine

[Anirban Ghosh]

On Tue, May 8, 2012 at 1:01 PM, rama david <ramadavidgroup at gmail.com> wrote:

>
>
> On Tue, May 8, 2012 at 1:00 PM, rama david <ramadavidgroup at gmail.com>wrote:
>
>> Hi Gromacs user,
>>              I am doing the justin tutorial on lipid posted on link......
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
>>
>> I am following the tutorial very carefully ...
>> As mentioned in the tutorial I need to generate strong position
>> restrained  on
>> proteins heavy atoms to ensure that position of atom does not change
>> during EM
>> (Energy Minimisation )
>> My command line is as follow .....
>>
>> genrestr  -f KALP_newbox.gro -o strong_posre.itp -fc 100000 100000 100000
>>
>>
>>
>> Reading structure file
>> Select group to position restrain
>> Group     0 (         System) has   138 elements
>> Group     1 (        Protein) has   138 elements
>> Group     2 (      Protein-H) has   109 elements
>> Group     3 (        C-alpha) has    16 elements
>> Group     4 (       Backbone) has    48 elements
>> Group     5 (      MainChain) has    64 elements
>> Group     6 (   MainChain+Cb) has    78 elements
>> Group     7 (    MainChain+H) has    81 elements
>> Group     8 (      SideChain) has    57 elements
>> Group     9 (    SideChain-H) has    45 elements
>> Select a group:
>>
>>
>>
>> I am using Gromacs 4.5.4
>>
>> Generally position restrain is applied on backbone of protein
>> So I choose backbone (4)
>>
>> Is it right or I have to choose the group protein(138 elements) to apply
>> position restraine on all protein atoms....
>>
>>
As the tutorial suggest you can restrain the heavy atoms, but I usually
restrain the entire protein during the InflateGro steps (EMs) and let the
lipids minimize around it.

-Anirban


>
>>
>>    All suggestions are welcome
>>    thank you in advance
>>
>>
>> Rama David .
>>
>>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120508/9ee46aa8/attachment.html>