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 -- 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
