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shirtsgroup / InterMol

Conversion tool for molecular simulations
MIT License
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Gromacs to AMBER ligand conversion #393

Open mmagithub opened 1 year ago

mmagithub commented 1 year ago

Hi,

I am trying to convert a qforce generated itp/gro/top files to amber prmtop file with intermol, but I keep getting the following error:

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 ?

I am attaching the files I want to convert.

Thanks, Marawan

fixed_h_lig2_qforce.itp.txt gas.top.txt gas.gro.txt

mattwthompson commented 1 year ago

That looks like a warning, not an error. It's telling you exactly what's happening - some lines are missing from your [ pairs ] directive compared to what ParmEd expects. This is the section where GROMACS handles 1-4 interactions, since they're missing it's assumed they're 0, which may or may not be what you intended to happen. For more see the GROMACS docs (keywords [ pairs ], 1-4, gen-pairs) or possibly the ParmEd issue tracker or source code.

mmagithub commented 1 year ago

Attempting to avoid the warning message with the (-f) option, I got the error:

TypeError: ChamberParm does not support all potential terms defined in the input Structure INFO 2023-03-22 12:36:29 Finished!

In both cases (with or without -f) it simply gives gromacs outputs, even though I am specifying output in an AMBER format.

mmagithub commented 1 year ago

According to the qforce developers (see attached outputs), all terms do exist in the qforce written outputs

mattwthompson commented 1 year ago

What command are you running?

selimsami commented 1 year ago

Hi, just to pitch in here. With respect to how GROMACS works, nothing is missing in these files:

1) [pairs] section is there on the bottom of the .itp file. 2) gen-pairs is turned on, therefore pair interactions should be set using the fudgeLJ and fudgeQQ rules.

I just tried running Marawan's files in GROMACS, and all interaction terms are well recognized.

Cheers, Selim

mmagithub commented 1 year ago

@mattwthompson

I am running this command: python ~/InterMol/intermol/convert.py --gro_in gas.top gas.gro --amber

Please look at this thread from Jason Swails at Parmed: https://github.com/ParmEd/ParmEd/issues/1298#issuecomment-1480117408

Do you believe there is a workaround?