Hi,
I'm trying to create virtual atoms for the hydrogens in a glycosylated protein,
specifically the hydrogens on the sugar. I have three types of hydrogens bound
to carbon: CH on ring carbon, CH2 on branched carbon, CH3 methyl group. I also
have OH and NH hydrogens.
Three questions:
1. Should all of these be 4fd type hydrogens because they are all ~sp3
hybridized geometry around the carbon (puckered ring, branched, methyl)?
2. I understand that I'll have to add a line like the following for each of my
virtual atoms. Can somebody please clarify what function 1 is, and what the
a,b and d parameters are?
[ virtual sites4 ]
; Site from funct a b d
5 1 2 3 4 1 0.33333 0.33333 -0.105
3. What is the best way to handle the OH and NH hydrogens?
Thank you for any advice!
Relly
_________________________________________________________________
Express your personality in color! Preview and select themes for HotmailĀ®.
http://www.windowslive-hotmail.com/LearnMore/personalize.aspx?ocid=TXT_MSGTX_WL_HM_express_032009#colortheme
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php