I was also trying to put more than one protein in one simulation box. I was able to do it with genconf but it appears that the addition is in very ordered manner if one looks .gro file in VMD. How can I add these protein in disordered random orientation. msnayeem
On 4/20/10, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > > fahimeh bafti wrote: > >> Thanks :) >> 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 >> > > editconf should not have a problem placing multi-residue molecules within a > box. That is its main function, so I can only assume you did something > wrong. > > I did it at the end with genconf >> >> genconf -nbox 2 2 2 (as u want) -f file.gro -o file_replicate.pdb >> >> it will simply replicate the unit. >> >> > That works. Glad you found a solution. > > -Justin > > Fahimeh >> >> > Date: Tue, 20 Apr 2010 09:12:44 -0400 >> > From: jalem...@vt.edu >> > To: gmx-users@gromacs.org >> > Subject: Re: [gmx-users] genbox >> > >> > >> > >> > fahimeh bafti wrote: >> > > Thank you Justin >> > > 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 >> > > genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb >> > > >> > > but it gave me: >> > > >> > > Fatal error: >> > > more then one residue in insert molecules >> > > program terminated >> > > >> > >> > Then you have two options: >> > >> > 1. Use the development (git) version of the code, which I believe can >> now deal >> > with multi-residue molecules. >> > 2. Use editconf to position all the components of your system. >> > >> > You could, I suppose, hack your "insert.pdb" to contain one residue >> (i.e., >> > through renaming and renumbering) and then convert it back, but that >> sounds like >> > a mess. Probably #2 is the easiest. >> > >> > -Justin >> > >> > > Fahimeh >> > > >> > > >> > > > Date: Tue, 20 Apr 2010 07:10:59 -0400 >> > > > From: jalem...@vt.edu >> > > > To: gmx-users@gromacs.org >> > > > Subject: Re: [gmx-users] genbox >> > > > >> > > > >> > > > >> > > > fahimeh bafti >> > > > > Hello, >> > > > > >> > > > > I want to use a file.pdb which has 8 chain of polypeptide, each >> chain >> > > > > contains 6 residues. I need to expand it to 12 chains of 6 >> rsidues >> > > so I >> > > > > need to add 4 chains or in the other word 24 residues. I think I >> > > have to >> > > > > use genbox, so I make another copy of file.pdb and rename it to >> > > > > insert.pdb and i used this command, but it doesn't work. >> > > > > >> > > > > genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro >> > > > > >> > > > > can anybody help me? >> > > > >> > > > The implication with genbox -ci -nmol is that the coordinate file >> > > passed to -ci >> > > > contains one molecule, and an additional -nmol molecules are >> > > inserted. So if >> > > > you already have 8, you need a coordinate file with one polypeptide >> > > and then: >> > > > >> > > > genbox -ci insert.pdb -nmol 4 >> > > > >> > > > Note in the documentation that -nmol refers to the number of >> > > molecules, not a >> > > > number of residues, which I think is the root of your problem. >> > > > >> > > > -Justin >> > > > >> > > > > >> > > > > Fahimeh >> > > > > >> > > > > >> > > >> ------------------------------------------------------------------------ >> > > > > Hotmail: Trusted email with powerful SPAM protection. Sign up >> now. >> > > > > <https://signup.live.com/signup.aspx?id=60969> >> > > > > >> > > > >> > > > -- >> > > > ======================================== >> > > > >> > > > Justin A. Lemkul >> > > > Ph.D. Candidate >> > > > ICTAS Doctoral Scholar >> > > > MILES-IGERT Trainee >> > > > Department of Biochemistry >> > > > Virginia Tech >> > > > Blacksburg, VA >> > > > jalemkul[at]vt.edu | (540) 231-9080 >> > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> > > > >> > > > ======================================== >> > > > -- >> > > > gmx-users mailing list gmx-users@gromacs.org >> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > > > Please search the archive at http://www.gromacs.org/search before >> > > posting! >> > > > Please don't post (un)subscribe requests to the list. Use the >> > > > www interface or send it to gmx-users-requ...@gromacs.org. >> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > >> > > >> ------------------------------------------------------------------------ >> > > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. >> Sign >> > > up now. <https://signup.live.com/signup.aspx?id=60969> >> > > >> > >> > -- >> > ======================================== >> > >> > Justin A. Lemkul >> > Ph.D. Candidate >> > ICTAS Doctoral Scholar >> > MILES-IGERT Trainee >> > Department of Biochemistry >> > Virginia Tech >> > Blacksburg, VA >> > jalemkul[at]vt.edu | (540) 231-9080 >> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> > >> > ======================================== >> > -- >> > gmx-users mailing list gmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at http://www.gromacs.org/search before >> posting! >> > Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to gmx-users-requ...@gromacs.org. >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> ------------------------------------------------------------------------ >> Hotmail: Powerful Free email with security by Microsoft. Get it now. < >> https://signup.live.com/signup.aspx?id=60969> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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