Thanks Justin for the quick reply. by the way after i solvated the protein with water and i change the amount of the protein that i want for example 8 and the amount of water that already in is 20453.But after i proceed with grompp the result shows that my .top file have different number of configuration with the solvation, .gro file. In addition when i view the file with vmd it still show only one protein and not the exact amount that i want.Well i'm kinda lost because after pdb2gmx for the single molecule and i separate the topology file with the .itp protein,the itp file still consist of 1 protein not 8 proteins right?
On Fri, Sep 6, 2013 at 10:13 AM, Justin Lemkul [via GROMACS] <ml-node+s5086n5011001...@n6.nabble.com> wrote: > > > On 9/5/13 10:09 PM, Nur Syafiqah Abdul Ghani wrote: > >> Hi all, >> >> Need your help to explain more about this multiple chain.I would like >> to do a simulation with a multiple type identical protein. By using >> the instruction that gromacs wrote in >> 'http://www.gromacs.org/Documentation/How-tos/Multiple_Chains', seem >> that i'm a bit lost when it tells us to us the .top file for grompp >> input and need to change the coordinate..Any one had facing this time >> problem? >> >> Btw i already do the pdb2gmx command for single protein and only don't >> understand after i put the number of amount of protein that i want in >> .top file. >> > > The number of molecules in the .top must correspond to a configuration you > have > built that has the same number of molecules. You can position molecules in > the > unit cell using editconf and the various options it provides (centering, > translation, rotation). > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > 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 > > [hidden email] | (410) 706-7441 > > ================================================== > -- > gmx-users mailing list [hidden email] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [hidden email]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > ________________________________ > If you reply to this email, your message will be added to the discussion > below: > http://gromacs.5086.x6.nabble.com/multiple-chain-tp5011000p5011001.html > To start a new topic under GROMACS Users Forum, email > ml-node+s5086n4370410...@n6.nabble.com > To unsubscribe from GROMACS, click here. > NAML -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. alternative email : syafiqahabdulgh...@gmail.com @ gs33...@mutiara.upm.edu.my -- View this message in context: http://gromacs.5086.x6.nabble.com/multiple-chain-tp5011000p5011002.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
