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

Vitaly Chaban chaban at univer.kharkov.ua
Fri Aug 1 13:41:34 CEST 2008

>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

>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.

When running genbox for the last time you can specify the length of
the each box side '-box'. It will enlarge your box and add the
corresponding solvent to this space.

Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban

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