[gmx-users] simulating several proteins

[Cristiano De Michele]

thank you very much for the useful hints!

Cristiano

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.
>
> -Justin
>
>> 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  
>>>> configuration
>>>> 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.
>>>
>>> Mark
>>> -- 
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> 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 gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>> ––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
>> 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
>> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>

––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
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
homepage: http://pacci.phys.uniroma1.it/
------
"Shoot for the moon. Even if you miss, you'll land among the stars."