Re: [gmx-users] Creation of an index file with seperate lipid leaflets
Thanks to all for your help/suggestions. I gave up on modifying make_ndx, the code is just too impenetrable for a weekend scripter like me... Have made a perl script to produce a .ndx file with 2 groups, one containing all upper leaflet atoms, the other lower. --- Patrick Fuchs [EMAIL PROTECTED] wrote: Hi, I've written a python script that does what you want. I cleaned the script (make_2leaflets_index) and put it on my web page at the following URL: http://condor.ebgm.jussieu.fr/~fuchs/download/index.html Hope it helps. Ciao, Patrick Jay Mashl a écrit : Wasted work would be bad ;) Rather than headgroup orientation, maybe try looking at atom distributions along the bilayer normal direction. Neutron scattering experiments show that for atom groups far from the bilayer midplane, the corresponding z-coordinates form two distinct distributions. So one way could be the following. Pick a headgroup atom and obtain its z-coordinate. Have make_ndx accept this value as input. Search the system by looping over lipids and ask whether that atom type has a z-coordinate within some amount around the input value. From this you know the membership of the leaflets. A more automatic way would be to have the program first discern the distribution and then reread the system to decide the leaflet membership. Jay On Wed, 8 Nov 2006, Alan Dodd wrote: Wouldn't shuffle/sort undo all the good work? I did wonder if I should have labelled the lipids in different leaflets as different molecule types, or different chains, but it's a bit late now... --- Jay Mashl [EMAIL PROTECTED] wrote: On Wed, 8 Nov 2006, Alan Dodd wrote: Has anyone already created a way to generate an index file with the atoms from the two leaflets of a bilayer listed seperately? I can't believe it hasn't already been done, but can't find a direct description of a solution. I'm attempting a modification to make_ndx, (or perhaps something considerably less ambitious, judging by the way it's going so far) to permit lipid selection based on headgroup orientation, though I'd quite like to save myself the effort. Incidentally, splitres and splitat seem to be the wrong way around, unless I'm misunderstanding them - they do the opposite of what they say. From the gromacs 3.3.1 source download I did on April of this year. Reordering the lipids into leaflets in your starting coordinate file might be a good idea. If you anticipate lipid exchange between leaflets, then a more general tool like what you suggest would be helpful. Jay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 Sponsored Link Mortgage rates near 39yr lows. $420k for $1,399/mo. Calculate new payment! http://www.LowerMyBills.com/lre ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] Creation of an index file with seperate lipid leaflets
Hi, I've written a python script that does what you want. I cleaned the script (make_2leaflets_index) and put it on my web page at the following URL: http://condor.ebgm.jussieu.fr/~fuchs/download/index.html Hope it helps. Ciao, Patrick Jay Mashl a écrit : Wasted work would be bad ;) Rather than headgroup orientation, maybe try looking at atom distributions along the bilayer normal direction. Neutron scattering experiments show that for atom groups far from the bilayer midplane, the corresponding z-coordinates form two distinct distributions. So one way could be the following. Pick a headgroup atom and obtain its z-coordinate. Have make_ndx accept this value as input. Search the system by looping over lipids and ask whether that atom type has a z-coordinate within some amount around the input value. From this you know the membership of the leaflets. A more automatic way would be to have the program first discern the distribution and then reread the system to decide the leaflet membership. Jay On Wed, 8 Nov 2006, Alan Dodd wrote: Wouldn't shuffle/sort undo all the good work? I did wonder if I should have labelled the lipids in different leaflets as different molecule types, or different chains, but it's a bit late now... --- Jay Mashl [EMAIL PROTECTED] wrote: On Wed, 8 Nov 2006, Alan Dodd wrote: Has anyone already created a way to generate an index file with the atoms from the two leaflets of a bilayer listed seperately? I can't believe it hasn't already been done, but can't find a direct description of a solution. I'm attempting a modification to make_ndx, (or perhaps something considerably less ambitious, judging by the way it's going so far) to permit lipid selection based on headgroup orientation, though I'd quite like to save myself the effort. Incidentally, splitres and splitat seem to be the wrong way around, unless I'm misunderstanding them - they do the opposite of what they say. From the gromacs 3.3.1 source download I did on April of this year. Reordering the lipids into leaflets in your starting coordinate file might be a good idea. If you anticipate lipid exchange between leaflets, then a more general tool like what you suggest would be helpful. Jay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 Sponsored Link Mortgage rates near 39yr lows. $420k for $1,399/mo. Calculate new payment! http://www.LowerMyBills.com/lre ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
[gmx-users] Creation of an index file with seperate lipid leaflets
Has anyone already created a way to generate an index file with the atoms from the two leaflets of a bilayer listed seperately? I can't believe it hasn't already been done, but can't find a direct description of a solution. I'm attempting a modification to make_ndx, (or perhaps something considerably less ambitious, judging by the way it's going so far) to permit lipid selection based on headgroup orientation, though I'd quite like to save myself the effort. Incidentally, splitres and splitat seem to be the wrong way around, unless I'm misunderstanding them - they do the opposite of what they say. From the gromacs 3.3.1 source download I did on April of this year. Alan Dodd University of Bristol __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] Creation of an index file with seperate lipid leaflets
On Wed, 8 Nov 2006, Alan Dodd wrote: Has anyone already created a way to generate an index file with the atoms from the two leaflets of a bilayer listed seperately? I can't believe it hasn't already been done, but can't find a direct description of a solution. I'm attempting a modification to make_ndx, (or perhaps something considerably less ambitious, judging by the way it's going so far) to permit lipid selection based on headgroup orientation, though I'd quite like to save myself the effort. Incidentally, splitres and splitat seem to be the wrong way around, unless I'm misunderstanding them - they do the opposite of what they say. From the gromacs 3.3.1 source download I did on April of this year. Reordering the lipids into leaflets in your starting coordinate file might be a good idea. If you anticipate lipid exchange between leaflets, then a more general tool like what you suggest would be helpful. Jay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] Creation of an index file with seperate lipid leaflets
Wouldn't shuffle/sort undo all the good work? I did wonder if I should have labelled the lipids in different leaflets as different molecule types, or different chains, but it's a bit late now... --- Jay Mashl [EMAIL PROTECTED] wrote: On Wed, 8 Nov 2006, Alan Dodd wrote: Has anyone already created a way to generate an index file with the atoms from the two leaflets of a bilayer listed seperately? I can't believe it hasn't already been done, but can't find a direct description of a solution. I'm attempting a modification to make_ndx, (or perhaps something considerably less ambitious, judging by the way it's going so far) to permit lipid selection based on headgroup orientation, though I'd quite like to save myself the effort. Incidentally, splitres and splitat seem to be the wrong way around, unless I'm misunderstanding them - they do the opposite of what they say. From the gromacs 3.3.1 source download I did on April of this year. Reordering the lipids into leaflets in your starting coordinate file might be a good idea. If you anticipate lipid exchange between leaflets, then a more general tool like what you suggest would be helpful. Jay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 Sponsored Link Mortgage rates near 39yr lows. $420k for $1,399/mo. Calculate new payment! http://www.LowerMyBills.com/lre ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] Creation of an index file with seperate lipid leaflets
Wasted work would be bad ;) Rather than headgroup orientation, maybe try looking at atom distributions along the bilayer normal direction. Neutron scattering experiments show that for atom groups far from the bilayer midplane, the corresponding z-coordinates form two distinct distributions. So one way could be the following. Pick a headgroup atom and obtain its z-coordinate. Have make_ndx accept this value as input. Search the system by looping over lipids and ask whether that atom type has a z-coordinate within some amount around the input value. From this you know the membership of the leaflets. A more automatic way would be to have the program first discern the distribution and then reread the system to decide the leaflet membership. Jay On Wed, 8 Nov 2006, Alan Dodd wrote: Wouldn't shuffle/sort undo all the good work? I did wonder if I should have labelled the lipids in different leaflets as different molecule types, or different chains, but it's a bit late now... --- Jay Mashl [EMAIL PROTECTED] wrote: On Wed, 8 Nov 2006, Alan Dodd wrote: Has anyone already created a way to generate an index file with the atoms from the two leaflets of a bilayer listed seperately? I can't believe it hasn't already been done, but can't find a direct description of a solution. I'm attempting a modification to make_ndx, (or perhaps something considerably less ambitious, judging by the way it's going so far) to permit lipid selection based on headgroup orientation, though I'd quite like to save myself the effort. Incidentally, splitres and splitat seem to be the wrong way around, unless I'm misunderstanding them - they do the opposite of what they say. From the gromacs 3.3.1 source download I did on April of this year. Reordering the lipids into leaflets in your starting coordinate file might be a good idea. If you anticipate lipid exchange between leaflets, then a more general tool like what you suggest would be helpful. Jay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 Sponsored Link Mortgage rates near 39yr lows. $420k for $1,399/mo. Calculate new payment! http://www.LowerMyBills.com/lre ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- R. Jay Mashl University of Illinois [EMAIL PROTECTED] (Tel)217-244-5818 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
