This might help:

https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2015-2016/0886.html

Hi, I was facing this error while running minimization using coarse-grain (MartiniFF in NAMD). Please check your corrected psf file (cg-fixed.psf). If backbone bead (BAS) has P4 or P5 (alone) generic type, you will get "unable to find bond or angle parameter error"

Dear Vinnarasi Saravanan I found that mainly alanine residues has backbone bead (BAS) P4 but P5C backbone bead (BAS) is present in various amino acids in psf. Please suggest how we can solve this issue.

Thanks

Hi Varun Dewaker , I fixed it for my system. First of all, find out where ALA (P4-246 atom) is present in your protein. For ex. ALA (only P4) could be place in any one of them in the following

1. in coil

2. Helix

3. N-terminal

4. C-terminal

5. Strand (or Trun)

6. Bend

7. Beta sheet (or extended)

After you figure it out, please look at the martini-protein.top file. You can get ALA bead type from there. If you have doubt, let me know.

Thanks

Hi Vinnarasi Saravanan , your suggestions worked very well. Thanks for your valuable time and taking part in the discussion.

Thanks Martin Klvana for taking part in the discussion.