[gmx-users] InflateGRO and trimer simulation

[KM]

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