On 7 May 2008 07:10:11 -0000 "minnale " <[EMAIL PROTECTED]> wrote:
Hi all, it may be trivial question My protien contain nearly 200 residues, I want plot RMSD for 45 to 90 residues , So I made make_ndx file also, but I am doubting that what i have I done whether right ot wrong? I have selcted 1 | r 45-90 1 = protein , the way I have selected is correct or I have to select 3 | r 45-90 3 = C-alpha
This won't give you what you want. you have to use 1 & r 45-90 : all protein atoms whithin residues 45-90 or 3 & 45-90 : all Ca atoms within residue 45-90 the sign "|" adds up the two groups the sign "&" take the intersection between the groups
you could do the check yourself, by editing the output index it and verify that the atom numbers given are or not what you want.
Pls tell me Thanks in advance
----------------------------------------------------- XAvier Periole - PhD NMR & Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole ----------------------------------------------------- _______________________________________________ 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
