Dear Justin, I have tried the command genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro but it got hanged. Is there something wrong with the command?
On Mon, Jun 9, 2014 at 5:50 PM, 陈功 <gchen...@gmail.com> wrote: > Thanks for correction. i appriciate it :) > Chen Gong > > > > > > From: Justin Lemkul > Date: 2014-06-09 19:58 > To: gmx-users > Subject: Re: [gmx-users] Regarding membrane construction > > > On 6/9/14, 3:22 AM, 陈功 wrote: > > Dear Venkat, I guess there are some other methods to generate new lipid > > bilayer construct by using genbox -cp your_membrane_protein -ci > lipid_monomer > > -nmol xxxcalculate by yourself -try 1000 -cs solovents.gro -p top.top -o > > new_conf.gro or using editconf & cat ...Another way, you can try the > script > > packmol. Be more patient. haha, I m also a new gmx user. Good luck, > chen > > Packmol is a good choice, but the approach above with genbox likely won't > work. > It will produce a random insertion of lipids. The simplest way within > Gromacs > to create a membrane of sufficient size is to place the protein in a > suitably > sized box (with editconf) and then > > genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
