Thank you Vandana and Justin, the cat command solve the problem. Regarding the removement of the unnecessary lines in the middle, is there a command that can do it automatically? or one has to make code by self? Thanks.
Yan On Tue, May 25, 2010 at 3:25 PM, Justin A. Lemkul <[email protected]> wrote: > > > VANDANA KUMARI wrote: > >> Hi Yan, >> >> You can do it by converting your both gro file into pdb files and >> concatenating both pdb files into one file . and you can convert pdb into >> gro using editconf >> steps are as follows: >> >> 1. editconf -f 1.gro -o 1.pdb >> 2. editconf -f 2.gro -o 2.pdb >> >> 3. cat 1.pdb 2.pdb > both.pdb >> >> you need to delete unnecessary line i.e. CRYST1 or END from you both.pdb >> file >> >> 4. editconf -f both.pdb -o both.gro >> > > Conversion back and forth between .pdb and .gro is not required (but it > does work). The main point of creating a concatenated file is that both > molecules are placed correctly within the same box, so for each: > > editconf -f 1.gro -o 1_newbox.gro -center x y z -box x y z > (and the same for molecule 2) > > Getting the molecule positions and box vectors right is the real trick. > > Then concatenate, remove unnecessary box and header lines in the middle of > the file, correct the atom count and you're done. > > -Justin > > > >> >> -- >> Vandana Kumari >> ------------------------------------------------------------------------ >> *From:* [email protected] [[email protected]] on >> behalf of Yan Gao [[email protected]] >> *Sent:* Tuesday, May 25, 2010 5:33 PM >> *To:* Discussion list for GROMACS users >> *Subject:* [gmx-users] How to combine two gro files in one big file >> >> Hi there, >> >> I want to simulate two molecules which are identical, and one is >> rotated/translated from another. I have the gro file for one molecule. >> >> I tried editconf, which helped manipulate the molecule. Then I want to >> combine it with the original gro file, so that the two identical molecules >> are placed in one file. I searched the manual but could not find a proper >> command. Could anyone help? Thanks. >> >> -- >> Yan >> >> > -- > ======================================== > > 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/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/mailing_lists/users.php > -- Yan Gao Jacobs School of Engineering University of California, San Diego Tel: 858-952-2308 Email: [email protected]
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