[gmx-users] About Merging topologies

Justin Lemkul jalemkul at vt.edu
Sat Apr 13 16:52:05 CEST 2013

On Sat, Apr 13, 2013 at 10:42 AM, vidhya sankar <scvsankar_agr at yahoo.com>wrote:

> Dear Justin thank you for your reply,
>                                                              Is there is
> Any tool  to merge topology of CNT (generated by g_x2top tool)  and Cyclic
> Peptide ( created by pdb2gmx) . otherwise Mere copy and Pasting the
> Corresponding Entries of CNT ( atom, Bond ,Angle, Dihedral Section)  to
> topology of Cyclic peptide
> Also Should  i Combine .RTP of CNT & .RTP of Cyclic Peptide for My system
> (My system CNT wrapped By cyclic Peptide )
> How to combine ?
> Mere Coy and Editing ( Changing Number and Oder)  and put it .RTP data
> base
Any topology can be included in a .top if it is converted to an .itp file
by removing the force field #include statement, [system] directive, and
[molecules] directive. Then just #include the new .itp file. This is
effectively what every pdb2gmx-generated topology does with ions, water,
etc. You have a CNT, which can be viewed as just another solute in the
system, so just #include its parameters after proper conversion from .top
to .itp.




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)


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