I want to simulate a RNA molecule in which first residue has a 5'-PO4 cap, which is uncommon. I want to add atom and bond parameters in the .rtp files but the changes are not getting saved. How can I append these parameters in existing .rtp files. I am using amber99 force field.
See my reply on the gmx-users mailing list. Modifying the .rtp file is an inefficient way to solve this problem.
See my reply on the gmx-users mailing list. Modifying the .rtp file is an inefficient way to solve this problem.
Hi
If you want to permanently change a rtp file, just copy the entire force field directory in your simulation folder and make all changes. Then when you are making the topology using the pdb2gmx you will see the local force field as first option in the list.
I cannot find your replies on the gmx-users mailing list. Would you like to share the link kindly? Justin Lemkul
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