[gmx-users] Re: Putting more than one peptide

[Justin A. Lemkul]

alkasrivastava at iitb.ac.in wrote:
> Hi
> 
> I am doing 5 peptide simulation.
> 
> 1. First i am defining a box using editconf
> 
> editconf -f 1st.gro -o box1.gro -bt cubic -box 6 -d 1.1
> 
> then for inserting the next peptide i am using genbox
> 
> genbox -cp box1.gro -ci 2nd.gro -nmol 1 -o box2.gro -seed 24 -try 100
> 
> and same for the subsequent 3 peptides.
> 
> So in this way when i am starting with first peptide i am giving -d option
> in editconf for defining the distance between the peptide and the box but
> i can not do this when i am inserting 2nd peptide and subsequent 3
> peptides.
> 

Run editconf again after you have inserted all of your peptides.

-Justin

> I am not very sure that if it is correct or not. Also i am not finding any
> option in genbox for -d during insertion.
> 
> Please suggest what is the best way.
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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
> 

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================