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

Sheyore Omovie omovie_johnnie at hotmail.com
Sat Aug 2 02:16:56 CEST 2008

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: chaban at univer.kharkov.ua> To: gmx-users at gromacs.org> 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: chaban at univer.kharkov.ua> skype: vvchaban> _______________________________________________> 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
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