Hi, Thanks. Now I add TER after every peptide coordinates. But then when I used the command pdb2gmx -chainsep, it said "invalid command line argument: -chainsep". So I am wondering the version I use is different or something. My version is gromacs 4.0.7. Sincerely, Qian
----- Original Message ----- From: "Justin A. Lemkul" <[email protected]> Date: Wednesday, October 13, 2010 2:08 am Subject: Re: [gmx-users] top file for two seperate peptides To: Discussion list for GROMACS users <[email protected]> > > > Qian Wang wrote: > >Hi, > > I want to simulate two seperate peptids in one box. However, > when I use pdb2gmx to build the top file of this system, I found > that gromacs thought there is only one peptide because it added > bond, angle and other energy terms between the termius of these > two peptides. Is there any way to prevent this problem, or I > need to change the top file by hand? Thanks a lot. > > When pdb2gmx processes an input coordinate file, it will assume > the amino acid sequence is one continuous protein unless you > have either TER delimiters between the chains or the chain ID > (A, B, C...) changes. Then apply the appropriate option to > pdb2gmx -chainsep. > > -Justin > > > Sincerely, > >Qian > > > > -- > ======================================== > > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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