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

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 1 12:01:25 CEST 2008

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.


> 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.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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