<DIV>Dear Goette</DIV> <DIV> </DIV> <DIV>Thanks a lot for your helpful suggestion.</DIV> <DIV> </DIV> <DIV>Cheers<BR><BR><B><I>Maik Goette <mgoette@mpi-bpc.mpg.de></I></B> wrote:</DIV> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Hi<BR><BR>Try the -ff option of pdb2gmx, if you're not able to get it working.<BR>This less complicated.<BR>pdb2gmx -f pdb.pdb -ff ffG43a1<BR><BR>Should work<BR><BR>Regards<BR><BR>Maik Goette, Dipl. Biol.<BR>Max Planck Institute for Biophysical Chemistry<BR>Theoretical & computational biophysics department<BR>Am Fassberg 11<BR>37077 Goettingen<BR>Germany<BR>Tel. : ++49 551 201 2310<BR>Fax : ++49 551 201 2302<BR>Email : mgoette[at]mpi-bpc.mpg.de<BR>mgoette2[at]gwdg.de<BR>WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/<BR><BR><BR>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>> Respectfully<BR>> <BR>> */Mitra Kheirabadi <MITRAKHEIRABADI@YAHOO.COM>/* wrote:<BR>> <BR>> Dear Periola<BR>> <BR>> I appreciate your kindly help.<BR>> <BR>> Respectfully<BR>> <BR>> */Xavier Periole <X.PERIOLE@RUG.NL>/* wrote:<BR>> <BR>> On Tue, 8 Jan 2008 06:35:28 -0800 (PST)<BR>> Mitra Kheirabadi wrote:<BR>> > Dear Dr. Smith<BR>> ><BR>> > I want to run a virus phosphorylated protein by gromacs.<BR>> Furtunatly, you<BR>> >construct related force field by ffG43A1p name. I copied this<BR>> force field to<BR>> >top. file gromacs but when I constructed pdbgmx, there is no<BR>> any ffG43a1p to<BR>> >select. Could you help me?<BR>> > I be so grateful to receive any information about it.<BR>> <BR>> you must modify the file top/FF.dat and include the new force field.<BR>> <BR>> XAvier<BR>> <BR>>
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