I want to perform MD simulation of DMF using GROMACS by following the path of pdb2gmx command. But for that pdb file of DMF is required which is not provided in default gromacs directory.
Also, how can I generate its rtp file?
Hi,
You can download DMF coordinates from PubChem or Zinc database. PubChem provides SDF format files. After downloading, you can convert the SDF format to PDB format using OpenBabel or other source code. Then, you can generate an RTP file for DMF.
Check the GROMACS tutorial at http://www.mdtutorials.com/gmx/complex/02_topology.html.
Here they provide the procedure to generate an rtp parameter for a new molecule based on the force field.
Hope this will help you!
Hi Sarah Elhajj,
Do not forget the geometric optimization of the DMF structure
Good luck
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