Thanks alot Justin for your detailed explanation. On Mon, 08 Sep 2008 Justin A.Lemkul wrote : > > >minnale wrote: >>Thanks Justin for your reply >>you mean to say that C32 of glycerol involves in the palimotyl chain >>formation so call as sn1 chain similarly C12,C13 of glycerol involves in the >>oleyl chain formation so call as sn2. >>Am I correct? > >More or less, let's just get a few things straight. Numbering like C32, C12, >C13, etc. is a scheme devised to give sensible atomic numbering to all atoms >in a 50 (or more)-atom lipid, but is not the same numbering scheme applied in >conventional lipid numbering from Biochemistry lessons. To me, "C32" has >absolutely no bearing on "sn-1." > >Look at the structure of glycerol: > >CH2OH >| > HO--C--H >| >CH2OH > >The second carbon is a chiral center, and (as I was taught in Biochemistry), >that is where we derive the "sn" nomenclature: sn-2 = "stereospecific number >2." > >The other carbons are given the obvious numbers of 1 and 3. By convention, >the phosphate headgroup is assigned to carbon 3. Therefore, chain 1 is on the >"sn-1" carbon, and chain 2 is on "sn-2." > >-Justin > >>Thanks in advance. >> >>On Mon, 08 Sep 2008 Justin A.Lemkul wrote : >> > >> > >> >minnale wrote: >> >> Hi all, >> >>may be this is very basic query >> >>I want to calculate order parameters of popc. I have found in archives >> that make sn1.ndx(pamitoyl) and sn2.ndx(oleyl) of popc then feed these files >> to g_order command. Can anyone tell me that why pamitoyl call as sn1 and >> oleyl call as sn2? >> > >> >It derives from the numbering of the carbons on the glycerol backbone. >> > >> >-Justin >> > >> >>Thanks for your help. >> >> >> >> >> >> >> >>578x38_banner2.gif >> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL >> PROTECTED]/2606998_2599290/2602379/1?PARTNER=3&OAS_QUERY=null> >> >> >> >> >> >>------------------------------------------------------------------------ >> >> >> >>_______________________________________________ >> >>gmx-users mailing list [email protected] >> >>http://www.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 >> > >> >-- ======================================== >> > >> >Justin A. Lemkul >> >Graduate Research Assistant >> >Department of Biochemistry >> >Virginia Tech >> >Blacksburg, VA >> >jalemkul[at]vt.edu | (540) 231-9080 >> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> > >> >======================================== >> >> >> >>578x38_banner2.gif >><http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL >> PROTECTED]/2606998_2599290/2602379/1?PARTNER=3&OAS_QUERY=null> >> >> >>------------------------------------------------------------------------ >> >>_______________________________________________ >>gmx-users mailing list [email protected] >>http://www.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 > >-- ======================================== > >Justin A. Lemkul >Graduate Research Assistant >Department of Biochemistry >Virginia Tech >Blacksburg, VA >jalemkul[at]vt.edu | (540) 231-9080 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >========================================
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