Open mmagithub opened 1 year ago
I keep getting this error when converting the qforce files to amber prmtop with parmed:
raise TypeError('ChamberParm does not support all potential terms '
TypeError: ChamberParm does not support all potential terms defined in the input Structure
or intermol:
parmed.exceptions.GromacsWarning: 9 1-4 pairs were missing from the [ pairs ] section and were set to zero; make sure you know what you're doing! INFO 2023-03-21 14:48:38 Finished!
Any clue ?
Hi Marawan,
There is a PR (#62) to write amber files but the authors have not yet addressed my final concerns so it's kinda stuck there.
One option could be to have a look there and finalize that.
Alternatively, keep in mind that UB terms is simply writing a harmonic bond and a harmonic angle together:
[ angles ] ; ai aj ak f theta0 k_theta r0 k_bond 1 2 3 5 120.000 290.220 0.21704 11255.9
can simply be written as:
[bonds] ; ai aj f r0 k_bond 1 3 1 0.21704 11255.9
[ angles ]
; ai aj ak f theta0 k_theta
1 2 3 1 120.000 290.220
then your conversion tools should probably work.
Regarding your second comment, I am not exactly sure what that means - What kind of output does it produce and what exactly does it set to zero? Q-Force does write out [ pairs ] section and its parameters are read from [ nonbond_params ] section. Could you try to copy the contents of [ nonbond_params ] to a new section called [ pairtypes ] . If [pairtypes] is empty GROMACS reads this from [ nonbond_params ] , but maybe your conversion tool does not figure that out.
Thanks Selim, Just wondering if you have ever tried to do the conversion before, it may be straightforward to do using the right tool,
I have asked this question on parmed and intermol repositories and it does not seem that there is a straightforward solution,
Parmed: https://github.com/ParmEd/ParmEd/issues/1298#issuecomment-1479702088
Intermol: https://github.com/shirtsgroup/InterMol/issues/393#issuecomment-1479741587
And I am not a big fan of manually editing parameter files, you can easily mess up things and never know that there is a fundamental issue with the parameters.
I tried copying the sections as you said, it did not help, I am still getting the same error messages.
What tool do you use to write the qforce itp & top file, is it a tool you developed internally or you are using standard tools from gromacs or parmed ?
According to the parmed/intermol threads, it seems the topology files written by qforce are missing some parameters, namely the 1-4 interactions terms, would you please confirm that it is what is happening or if there is a better explanation for this behavior.
I'm afraid the AMBER file writing seems to be suck, there was some incompatibility between the functional forms I think. It should definitely be fixable but I never user AMBER, so I have no motivation or knowledge to take care of this. I might soon implement an OpenMM format though.
I am not sure if something useful came of the discussions in intermol/parmed githubs? What is it that you are currently stuck with regarding the conversion?
If it's just the RB dihedral type, I could make to option to write the dihedrals in Fourier format if this will allow for a successful conversion?
Thanks Selim, OpenMM format is also good. I will see how can I make the most use of Gromacs formatted files in my applications.
Hi,
I am wondering if there is a straightforward way to save amber compatible prmtop files, as attempting to convert the gromacs generated top/itp files is not straightforward due to the Urey-Bradley terms I am speculating, parmed cannot handle this conversion easily,
Thanks, Marawan