[gmx-users] InflateGRO and trimer simulation

[KM]

OK, now it works. :)

Chris

W dniu 10 stycznia 2010 20:06 użytkownik KM <mitomaster at gmail.com> napisał:
> Thank you!
> This is what I need, however I keep getting a lot of errors about
> uninitialized values. When the script finishes, the membrane is
> rescaled, but the protein is untouched in the corner of the new box :(
> I'll try to investigate a little bit despite I don't know perl,
> however I believe that knowledge of python, C and tcl will help me
> understand what's going on.
>
> Chris
>
> 2010/1/10 patrick fuchs <patrick.fuchs at univ-paris-diderot.fr>:
>> Hi,
>> the new inflategro with the 'doughnut mode'
>> (http://www.csb.bit.uni-bonn.de/inflategro.html) might do what you want.
>> Ciao,
>>
>> Patrick
>>
>> Justin A. Lemkul a écrit :
>>>
>>>
>>> On 1/10/10 5:17 AM, KM wrote:
>>>>
>>>> Hello Gromacs Users,
>>>>
>>>> I would like to run a simulation of a trimer in a DPPC membrane. I
>>>> really like the elegant solution that inflategro script offers,
>>>> however I'm afraid I won't be able to use it, because I need to have
>>>> lipids in a small space between the monomers right in the center of
>>>> the box and these will certainly get deleted during the whole
>>>> procedure. I also need to keep the waters that come with the structure
>>>> of the protein.
>>>> Do you have any idea how I can elegantly embed my trimer in a
>>>> membrane, possibly using somehow modified inflategro?
>>>>
>>>> Christopher
>>>
>>> I've built multimeric systems with InflateGRO, but with a lot less
>>> constraints than you have :)  You can, for instance, run an inflation step
>>> with a very minimal scaling factor (like 1.01 or 1.05) and a very small
>>> cutoff (7 or so, but you'd have to play around with this) so you essentially
>>> delete lipids in place without moving them too much.  I don't know if the
>>> necessary lipids between the monomers will be affected.
>>>
>>> As for preserving water molecules, you could probably just extract their
>>> coordinates from a suitably-oriented starting structure and paste them into
>>> the InflateGRO output.
>>>
>>> None of this requires modifying InflateGRO, but will likely require a lot
>>> of trial and error, if it even works, given the very specific nature of what
>>> you need.
>>>
>>> -Justin
>>>
>>
>> --
>> _______________________________________________________________________
>> !!!! new E-mail address: patrick.fuchs at univ-paris-diderot.fr !!!!
>> Patrick FUCHS
>> Dynamique des Structures et Interactions des Macromolécules Biologiques
>> INTS, INSERM UMR-S665, Université Paris Diderot,
>> 6 rue Alexandre Cabanel, 75015 Paris
>> Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31
>> Web Site: http://www.dsimb.inserm.fr/~fuchs
>> --
>> 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/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/mailing_lists/users.php
>>
>
>
>
> --
> "W każdej wsi jest pochodnia oświaty - nauczyciel - oraz gaśnica - ksiądz."
>
> Victor Hugo
>



-- 
"W każdej wsi jest pochodnia oświaty - nauczyciel - oraz gaśnica - ksiądz."

Victor Hugo