[gmx-users] how to add a repeat unit in the .rtp file

Rahul Karyappa r.karyappa at ncl.res.in
Sat Aug 20 07:10:42 CEST 2005

Dear all,
   I want to use Gromacs for the synthetic polymers. First I saved the model file in .pdb format and I generated .gro and .top files from PRODRG website. I included all the type of atoms and bonds in the .rtp file. This I did for 5 repeat units of chain. But if I increase the chain length I need to add more atoms and bonds in the .rtp file which is more time-consuming. PLease tell me how I can add the atoms and bonds for a single repeat unit and I can use it for any length of chain.
  In the generated topological or gromacs format the atoms are named in specific format like: For C atoms--- CAA, CAB ,CAC,.....CAI-- For H atoms---- HAA, HAB, ....., HAI.. Similarly for O atoms. For trial what I did is, I put in like this--CA*, HA*.... But it is showing error. How to put them in the .rtp file for a single repeat unit? Suggestions are welcome as early as possible. Thank you in advance.
Rahul Karyappa
NCL, Pune, India

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