[gmx-users] How to combine two gro files in one big file

[Yan Gao]

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 <jalemkul at vt.edu> 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:* gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
>> behalf of Yan Gao [y1gao at ucsd.edu]
>> *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
>
> ========================================
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-- 
Yan Gao
Jacobs School of Engineering
University of California, San Diego
Tel: 858-952-2308
Email: Yan.Gao.2001 at gmail.com
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