OK, now it works. :) Chris
W dniu 10 stycznia 2010 20:06 użytkownik KM <[email protected]> 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 <[email protected]>: >> 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: [email protected] !!!! >> 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 [email protected] >> 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 [email protected]. >> 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 -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
