<DIV>Hi,</DIV>
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<DIV>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. </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 2:08 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 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 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>