<DIV>Hi,</DIV>
<DIV> </DIV>
<DIV>It works. Thanks a lot.</DIV>
<DIV> </DIV>
<DIV>Sincerely,</DIV>
<DIV>Qian<BR><BR>----- Original Message -----<BR>From: "Justin A. Lemkul" <jalemkul@vt.edu><BR>Date: Wednesday, October 13, 2010 2:28 am<BR>Subject: Re: [gmx-users] top file for two seperate peptides<BR>To: Gromacs Users' List <gmx-users@gromacs.org><BR><BR>> <BR>> <BR>> Qian Wang wrote:<BR>> >Hi,<BR>> > Thanks. Now I add TER after every peptide coordinates. But <BR>> then when I used the command pdb2gmx -chainsep, it said "invalid <BR>> command line argument: -chainsep". So I am wondering the version <BR>> I use is different or something. My version is gromacs 4.0.7.<BR>> > <BR>> <BR>> The -chainsep option was introduced in version 4.5. With <BR>> older versions I think you should just be able to use -ter to <BR>> interactively assign the protonation state of the termini.<BR>> <BR>> -Justin<BR>> <BR>> >Sincerely,<BR>> >Qian<BR>> ><BR>> >----- Original Message -----<BR>> >From: "Justin A. Lemkul" <jalemkul@vt.edu><BR>> >Date: Wednesday, October 13, 2010 2:08 am<BR>> >Subject: Re: [gmx-users] top file for two seperate peptides<BR>> >To: Discussion list for GROMACS users <gmx-users@gromacs.org><BR>> ><BR>> > ><BR>> > ><BR>> > > Qian Wang wrote:<BR>> > > >Hi,<BR>> > > > I want to simulate two seperate peptids in one box. However,<BR>> > > when I use pdb2gmx to build the top file of this system, I found<BR>> > > that gromacs thought there is only one peptide because it added<BR>> > > bond, angle and other energy terms between the termius of these<BR>> > > two peptides. Is there any way to prevent this problem, or I<BR>> > > need to change the top file by hand? Thanks a lot.<BR>> > ><BR>> > > When pdb2gmx processes an input coordinate file, it will assume<BR>> > > the amino acid sequence is one continuous protein unless you<BR>> > > have either TER delimiters between the chains or the chain ID<BR>> > > (A, B, C...) changes. Then apply the appropriate <BR>> option to<BR>> > > pdb2gmx -chainsep.<BR>> > ><BR>> > > -Justin<BR>> > ><BR>> > > > Sincerely,<BR>> > > >Qian<BR>> > > ><BR>> > ><BR>> > > --<BR>> > > ========================================<BR>> > ><BR>> > > Justin A. Lemkul<BR>> > > Ph.D. Candidate<BR>> > > ICTAS Doctoral Scholar<BR>> > > MILES-IGERT Trainee<BR>> > > Department of Biochemistry<BR>> > > Virginia Tech<BR>> > > Blacksburg, VA<BR>> > > jalemkul[at]vt.edu | (540) 231-9080<BR>> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>> > ><BR>> > > ========================================<BR>> > > --<BR>> > > gmx-users mailing list gmx-users@gromacs.org<BR>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users<BR>> > > Please search the archive at<BR>> > > http://www.gromacs.org/Support/Mailing_Lists/Search before <BR>> posting!> > Please don't post (un)subscribe requests to the <BR>> list. Use the<BR>> > > www interface or send it to gmx-users-request@gromacs.org.<BR>> > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<BR>> <BR>> -- <BR>> ========================================<BR>> <BR>> Justin A. Lemkul<BR>> Ph.D. Candidate<BR>> ICTAS Doctoral Scholar<BR>> MILES-IGERT Trainee<BR>> Department of Biochemistry<BR>> Virginia Tech<BR>> Blacksburg, VA<BR>> jalemkul[at]vt.edu | (540) 231-9080<BR>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>> <BR>> ========================================<BR>> -- <BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://lists.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at <BR>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</DIV>