<div>Dear Mark</div> <div> </div> <div>Thank you very much for your helpful suggestions.</div> <div> </div> <div>sincerly<BR><BR><B><I>Mark Abraham <Mark.Abraham@anu.edu.au></I></B> wrote:</div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Mitra Kheirabadi wrote:<BR>> Dear Dr.Periole<BR>> <BR>> I add ffG43a1p to FF.dat/ top and changed 11 to 12 on this file but <BR>> sorry again I did not appear. please help me.<BR><BR>The new forcefield files have to go to the same location as the old <BR>ones, in the subdirectory something like share/gromacs/top. Or <BR>preferably, you can copy the contents of that directory to somewhere <BR>else, do your fiddling there, and set the environment variable GMXLIB to <BR>point to that new directory every time you want to use this modified <BR>forcefield. When you don't want this forcefield, unset GMXLIB and you <BR>will get back your pristine GROMACS
installation, and you can be <BR>confident you haven't broken things there!<BR><BR>Unless you have pre-built .itp files for the phosphorylated systems, it <BR>is likely you will need to define new residue types in an .rtp file. <BR>Copy and rename the ffG43a1 version, and modify to suit your planned <BR>residues. A sound knowledge of chapter 5 of the manual will be required.<BR><BR>Mark<BR>_______________________________________________<BR>gmx-users mailing list gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please search the archive at http://www.gromacs.org/search before posting!<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to gmx-users-request@gromacs.org.<BR>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR></BLOCKQUOTE><BR><p> 
<hr size=1>Never miss a thing. <a href="http://us.rd.yahoo.com/evt=51438/*http://www.yahoo.com/r/hs"> Make Yahoo your homepage.</a>