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Thank you Justin<br>but I end up with a new error. now in the insert.pdp file I have a molecule which I need to add 4 copy of that inside the solute.pdb<br>genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb <br><br>but it gave me: <br><br>Fatal error:<br>more then one residue in insert molecules<br>program terminated<br><br>Fahimeh<br><br><br>> Date: Tue, 20 Apr 2010 07:10:59 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] genbox<br>> <br>> <br>> <br>> fahimeh bafti <br>> > Hello,<br>> > <br>> > I want to use a file.pdb which has 8 chain of polypeptide, each chain <br>> > contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I <br>> > need to add 4 chains or in the other word 24 residues. I think I have to <br>> > use genbox, so I make another copy of file.pdb and rename it to <br>> > insert.pdb and i used this command, but it doesn't work.<br>> > <br>> > genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro<br>> > <br>> > can anybody help me?<br>> <br>> The implication with genbox -ci -nmol is that the coordinate file passed to -ci <br>> contains one molecule, and an additional -nmol molecules are inserted. So if <br>> you already have 8, you need a coordinate file with one polypeptide and then:<br>> <br>> genbox -ci insert.pdb -nmol 4<br>> <br>> Note in the documentation that -nmol refers to the number of molecules, not a <br>> number of residues, which I think is the root of your problem.<br>> <br>> -Justin<br>> <br>> > <br>> > Fahimeh<br>> > <br>> > ------------------------------------------------------------------------<br>> > Hotmail: Trusted email with powerful SPAM protection. Sign up now. <br>> > <https://signup.live.com/signup.aspx?id=60969><br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.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 />Hotmail: Trusted email with Microsoft’s powerful SPAM protection. <a href='https://signup.live.com/signup.aspx?id=60969' target='_new'>Sign up now.</a></body>
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