Hi, It works. Thanks a lot. Sincerely, Qian ----- Original Message ----- From: "Justin A. Lemkul" <[email protected]> Date: Wednesday, October 13, 2010 2:28 am Subject: Re: [gmx-users] top file for two seperate peptides To: Gromacs Users' List <[email protected]>
> > > Qian Wang wrote: > >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. > > > > The -chainsep option was introduced in version 4.5. With > older versions I think you should just be able to use -ter to > interactively assign the protonation state of the termini. > > -Justin > > >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 > > -- > ======================================== > > 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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