Another way arround it is to place all 5 peptides in a pdb file, separating
each with TER ( be sure the coordinates of d atoms are not d same); before
running editconf and genbox.> Date: Fri, 1 Aug 2008 14:41:34 +0300> From:
[EMAIL PROTECTED]> To: [email protected]> Subject: [gmx-users] Re: Putting
more than one peptide> > >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.> > >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: [EMAIL PROTECTED]>
skype: vvchaban> _______________________________________________> gmx-users
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