Hello everyone,
I am working on DNA with two covalently bound modified cholesterol chains. I am unable to make the pdb2gmx file. I have generated the itp and prm file using CGENFF python script. But, I am unable to proceed further as the rtp file for the modified cholesterol and the parameters required are not present. Can anybody tell me the procedure for generating the pdb2gmx file for DNA with the covalently bound ligand.
Thank you in advance
Hi,
basically you can not use pdb2gmx (only works for Proteins, DNA/RNA and some cofactors). You must 1) generate the modified system manually, or 2) generate two topologies and mannualy join them. When I have to generate such topologies, I use AmberTools to get the system and then convert it to GROMACS using ParMed.
- Badges
- Science topic
- Similar topics
- Filing