Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Problam:Providing the ITP file myself results in an error. #67

Open
kk-ssh opened this issue Oct 16, 2024 · 1 comment
Open

Problam:Providing the ITP file myself results in an error. #67

kk-ssh opened this issue Oct 16, 2024 · 1 comment
Assignees
Labels
question Further information is requested

Comments

@kk-ssh
Copy link

kk-ssh commented Oct 16, 2024

Dear @hernanchavezthielemann
I lost some force field parameters while using the autoload button. I tried to provide the force field parameters using the ITP file; however, since I only have one ITP file, I attempted to enter the required files for force field, non-bonded, and bonded as specified by the software. I encountered the following error: Dihedral potential problem found!! Adopting X-A1-A2-X configuration for: 1-2.
Here is my itp file.
Thank you for your assistance!
1.itp.json
3bon.itp.json
2nb.itp.json

@kk-ssh kk-ssh added the bug Something isn't working label Oct 16, 2024
@hernanchavezthielemann
Copy link
Owner

Dear Jing @kk-ssh,

Thank you for your question,
try always with the autoload, that is fine, I think I should remove the other option at this point, since the autoload is kind of mature.
I am not sure whether what you are getting there is an error, it looks to me like a warning (potential problem)

To better understand and check your error, I would need all your files ( .gro too)
if those are all your itps, then I think you are missing the defaults directive
this is an example of the defaults directive:

[ defaults ]
; nbfunc = 1 means to impose Lennard-Jones
; comb-rule = 3 means to provide sigma & epsilon
; fudgeQQ = 0.5 because we have electrostatic interacations
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5

you can find more about it in GROMACS manual, and bear in mind that the values are normaly given by the forcefield that you are using, so do not use something generic.

please let me know how it goes,
Best,
Hernan.

@hernanchavezthielemann hernanchavezthielemann added question Further information is requested and removed bug Something isn't working labels Oct 19, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
question Further information is requested
Projects
None yet
Development

No branches or pull requests

2 participants