Module 4 : Classical Molecular Dynamics using Gromacs
Chapter 35 : The formation of topology file of a molecule
 
35.1 Introduction

Here we are going to discuss how you can make a topology file of a molecule that is defined in the aminoacids.rtpfileand this file is present in the force field directory that is present in gromacs. You can see this file in the following directory 

cd home/user/gromacs-4.5.4/gro4.5.4/share/gromacs/top
<enter>
Then you will see following force field directories
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amber03.ff         atommass.dat  co-shift.dat      encadv.ff     ffG53a5.itp     flexspc.itp
gromos53a5.ffoplsaa.ff spc216.gro    table6-10.xvg  tip4p.itp
amber94.ff atom_nom.tbl  defselection.dat  export.dlg    ffG53a6.itp     flexwat-ferguson.itp
gromos53a6.ff phbres.dat        spce.itp      table6-11.xvg  tip5p.gro
amber96.ff bonds.dlg     dgsolv.dat        ffencads.itp  ffgmx2.itp
gmx2.ff gurgle.dat     ps.m2p            spc.itp       table6-12.xvg  vdwradii.dat
amber99.ff bromacs.dat   edissoc.dat       ffencadv.itp  ffgmx.itp
gmx.ff ha-shift.dat   random.dat        specbond.dat  table6-8.xvg   xlateat.dat
amber99sb.ff ca-shift.dat  electroneg.dat    ffG43a1.itp   ffoplsaa.itp    gromos43a1.ff         highway.dat    refi_aa.dat       ss.map        table6-9.xvg
amber99sb-ildn.ff cb-shift.dat  elements.dat      ffG43a2.itp   ffoplsaa-n.tst  gromos43a2.ff         ions.itp       residuetypes.dat  surface.dat   tip3p.itp
amberGS.ffcharmm27.ffencads.ff ffG45a3.itp   flexspce.itp    gromos45a3.ff         links.dat      sfactor.dat       sw.itp        tip4p.gro

Note: the directories are bold and underline.
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