[gmx-users] simulating several proteins
Cristiano De Michele
cristiano.demichele at roma1.infn.it
Thu Mar 11 14:52:51 CET 2010
thank you very much for the useful hints!
Il giorno 10/mar/10, alle ore 18:35, Justin A. Lemkul ha scritto:
> Cristiano De Michele wrote:
>> ok but after I generated two .gro files using genconf (or editconf
>> I guess)
>> containing two identical proteins in different positions/orientations
>> how can I concatenate these two files in order to supply a
>> unique .gro file to grompp?
> If you run genconf correctly, then it should give you a proper .gro
> file, i.e.:
> genconf -f oneprotein.gro -o twoprotein.gro -nbox 2 1 1
> The above command will give two replicates of your protein aligned
> along the x axis.
> If you have two unique orientations that you want to align, you can
> simply use editconf to assign their position within a box (with -
> center and -box simultaneously), and simply use the Unix 'cat'
> command to concatenate them. Then you have to update the second line
> of the .gro file to reflect the proper number of atoms and remove
> the superfluous headers and box vectors in the middle of the file.
>> thanks Cristiano
>> Il giorno 10/mar/10, alle ore 16:27, Mark Abraham ha scritto:
>>> ----- Original Message -----
>>> From: Cristiano De Michele <cristiano.demichele at roma1.infn.it>
>>> Date: Thursday, March 11, 2010 2:25
>>> Subject: [gmx-users] simulating several proteins
>>> To: gmx-users at gromacs.org
>>>> Dear all,
>>>> is it possible to simulate more than one protein with GROMACS?
>>>> I would like to simulate two lysozyme proteins not solvated and
>>>> I tried changing number of proteins in topology file (attached) and
>>>> then I used this modified .top file to generate a .gro
>>>> with genbox, but I always end up getting just one protein
>>>> in the simulation box...
>>> genbox doesn't take input from the .top file to guide its output.
>>> Use genconf on your original structure file to multiply it. Then
>>> edit your .top by hand to match.
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>> Cristiano De Michele, Ph.D.
>> Department of Physics Tel. :
>> University of Rome "La Sapienza" Fax : +39064463158
>> Piazzale Aldo Moro, 2
>> I-00185 Roma - Italy
>> homepage: http://pacci.phys.uniroma1.it/
>> "Shoot for the moon. Even if you miss, you'll land among the stars."
> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before
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Cristiano De Michele, Ph.D.
Department of Physics Tel. : +390649913524
University of Rome "La Sapienza" Fax : +39064463158
Piazzale Aldo Moro, 2
I-00185 Roma - Italy
"Shoot for the moon. Even if you miss, you'll land among the stars."
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