Gromacs to AMBER ligand conversion

[mmagithub]

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]

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]

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]

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

[mattwthompson]

What command are you running?

[selimsami]

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]

@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:
ParmEd/ParmEd#1298 (comment)

Do you believe there is a workaround?