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Thanks :)<br>but I couldn't manage with that, it makes the same error with editconf as well, the problem was related to having more than one residue inside insert.gro<br>I did it at the end with genconf <br><br>genconf -nbox 2 2 2 (as u want) -f file.gro -o file_replicate.pdb<br><br>it will simply replicate the unit.<br><br>Fahimeh<br><br>> Date: Tue, 20 Apr 2010 09:12:44 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] genbox<br>> <br>> <br>> <br>> fahimeh bafti wrote:<br>> > Thank you Justin<br>> > but I end up with a new error. now in the insert.pdp file I have a <br>> > 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>> <br>> Then you have two options:<br>> <br>> 1. Use the development (git) version of the code, which I believe can now deal <br>> with multi-residue molecules.<br>> 2. Use editconf to position all the components of your system.<br>> <br>> You could, I suppose, hack your "insert.pdb" to contain one residue (i.e., <br>> through renaming and renumbering) and then convert it back, but that sounds like <br>> a mess. Probably #2 is the easiest.<br>> <br>> -Justin<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 <br>> > so I<br>> > > > need to add 4 chains or in the other word 24 residues. I think I <br>> > 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 <br>> > passed to -ci<br>> > > contains one molecule, and an additional -nmol molecules are <br>> > inserted. So if<br>> > > you already have 8, you need a coordinate file with one polypeptide <br>> > and then:<br>> > ><br>> > > genbox -ci insert.pdb -nmol 4<br>> > ><br>> > > Note in the documentation that -nmol refers to the number of <br>> > 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>> > ------------------------------------------------------------------------<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 <br>> > 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>> > ------------------------------------------------------------------------<br>> > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign <br>> > up now. <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: Powerful Free email with security by Microsoft. <a href='https://signup.live.com/signup.aspx?id=60969' target='_new'>Get it now.</a></body>
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