[EMAIL PROTECTED] 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.
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--
========================================
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
========================================
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