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Another way arround it is to place all 5 peptides in a pdb file, separating each with TER ( be sure the coordinates of d atoms are not d same); before running editconf and genbox.<BR><BR>> Date: Fri, 1 Aug 2008 14:41:34 +0300<BR>> From: chaban@univer.kharkov.ua<BR>> To: gmx-users@gromacs.org<BR>> Subject: [gmx-users] Re: Putting more than one peptide<BR>> <BR>> >1. First i am defining a box using editconf<BR>> ><BR>> >editconf -f 1st.gro -o box1.gro -bt cubic -box 6 -d 1.1<BR>> ><BR>> >then for inserting the next peptide i am using genbox<BR>> ><BR>> >genbox -cp box1.gro -ci 2nd.gro -nmol 1 -o box2.gro -seed 24 -try 100<BR>> ><BR>> >and same for the subsequent 3 peptides.<BR>> ><BR>> >So in this way when i am starting with first peptide i am giving -d option<BR>> >in editconf for defining the distance between the peptide and the box but<BR>> >i can not do this when i am inserting 2nd peptide and subsequent 3<BR>> >peptides.<BR>> <BR>> >I am not very sure that if it is correct or not. Also i am not finding any<BR>> >option in genbox for -d during insertion.<BR>> <BR>> <BR>> When running genbox for the last time you can specify the length of<BR>> the each box side '-box'. It will enlarge your box and add the<BR>> corresponding solvent to this space.<BR>> <BR>> -- <BR>> Vitaly V. Chaban<BR>> School of Chemistry<BR>> National University of Kharkiv<BR>> Svoboda sq., 4, Kharkiv 61077, Ukraine<BR>> email: chaban@univer.kharkov.ua<BR>> skype: vvchaban<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><br /><hr />Stay in touch when you're away with Windows Live Messenger. <a href='http://www.windowslive.com/messenger/overview.html?ocid=TXT_TAGLM_WL_messenger2_072008' target='_new'>IM anytime you're online.</a></body>
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