Hello Agnivo,

You can use Automatic Topology Builder (ATB-server) to generate gromacs compatible topology of your modified nucleotide with modified United atom force fields. the process is rather simple, first you have to manually add the thiol moiety at the desired 5' and/or 3' end and then save the file in PDB format. or you can use the DRAW molecule function of ATB and/or provide a valid SMILES formula for your molecule. After that the server will provide you with all the FF parameters which you can add to Gromacs as a modified FF or use it from your directory.

Best

Raghav

You can start with online molecular designing web portals, get the structure, download it, than modify using pymol or use VMD for further modification. Now at this point you have a structure save it in pdb format, look for force filed in NAMD/GOMACS.

You may start with VMD too, they have provided plugin to design the structure like molfructure. It will take some time to start with these things, it will be better, if yu seek help from some expert before starting MD.

Mr. Gosai,

You can do this by GaussView (www.gaussview.com)

The files can be exported as *.mol; *.mol2; *.ml2, respectively.

you can use CHEMSKETCH.

You can't do much better than to use YASARA (go to their website). Excellent build tools, excellent graphics, analysis tools, MD (Amber). You can (almost certainly) also process GROMACS data using YASARA. Goog luck.

Dear Agnivo,

     How about the plugin 'FFTK' in VMD, and its output file can be used by NAMD directily.

Link  http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/

Best Wishes!

https://en.wikipedia.org/wiki/Molecular_design_software