# Pmx - problems reproducing benchmarking from de Groot 2020 **URL:** \ **Category:** pmx\ **Created:** [September 10, 2021, 11:46am UTC](https://ask.bioexcel.eu/t/pmx-problems-reproducing-benchmarking-from-de-groot-2020/3247 "2021-09-10T11:46:35Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![galmasrati](https://avatars.discourse-cdn.com/v4/letter/g/b9e5f3/32.png) [@galmasrati](https://ask.bioexcel.eu/u/galmasrati)\ **Post date:** [September 10, 2021, 11:46am UTC](https://ask.bioexcel.eu/t/pmx-problems-reproducing-benchmarking-from-de-groot-2020/3247/1 "2021-09-10T11:46:35Z")
Hi All, I’m trying to reproduce some of the TI benchmarking done in the following paper: “Large scale relative protein ligand binding affinities using non-equilibrium alchemy” using pmx and the data provided in the GiHub repository referred to in the paper. In order to produce the hybrid topology I did the following: Step 1: python one\_ff\_file.py -ffitp lig\_CHEMBL3402752\_30000\_12/ffMOL.itp lig\_CHEMBL3402748\_5300\_8/ffMOL.itp -ffitp\_out ffMOL.itp Step 2: python atoms\_to\_morph.py -i1 lig\_CHEMBL3402752\_30000\_12/mol\_gmx.pdb -i2 lig\_CHEMBL3402748\_5300\_8/mol\_gmx.pdb -o1 pairs.dat -alignment -H2H Step 3: python make\_hybrid.py -l1 lig\_CHEMBL3402752\_30000\_12/mol\_gmx.pdb -l2 lig\_CHEMBL3402748\_5300\_8/mol\_gmx.pdb -itp1 lig\_CHEMBL3402752\_30000\_12/MOL.itp -itp2 lig\_CHEMBL3402748\_5300\_8/MOL.itp -pairs pairs.dat -oa merged.pdb -oitp MOL.itp -ffitp ffmerged.itp -scDUMd 0.1 Step 4: python one\_ff\_file.py -ffitp ffMOL.itp ffmerged.itp -ffitp\_out ffMOL.itp However, I noticed that in step 2, the pairs.dat file that is being produced is different than the one provided with the benchmarking data. Specifically, the mapping of the atoms between the two ligands is different. All the input files and scripts I used are from the pmx GitHub repository and I made no changes. I run pmx on a mac within a conda environment with python2.7. Any suggestions on what could be the reason for these differences? The original pairs file can be found here: > **[pmx/protLig\_benchmark/cmet/transformations\_gaff2/edge\_CHEMBL3402752\_30000\_12\_CHE...](https://github.com/deGrootLab/pmx/tree/master/protLig_benchmark/cmet/transformations_gaff2/edge_CHEMBL3402752_30000_12_CHEMBL3402748_5300_8)** > > master/protLig\_benchmark/cmet/transformations\_gaff2/edge\_CHEMBL3402752\_30000\_12\_CHEMBL3402748\_5300\_8 The ligands pdb can be found at: [pmx/protLig\_benchmark/cmet/ligands\_gaff2/lig\_CHEMBL3402748\_5300\_8 at master · deGrootLab/pmx · GitHub](https://github.com/deGrootLab/pmx/tree/master/protLig_benchmark/cmet/ligands_gaff2/lig_CHEMBL3402748_5300_8) and lig\_CHEMBL3402752\_30000\_12 And my pairs.dat file looks like this: 1 1 2 2 3 6 4 5 5 4 6 3 7 7 8 8 9 9 10 10 11 11 12 12 13 13 14 14 15 15 16 16 17 17 18 18 19 19 20 20 25 22 27 21 28 28 32 33 33 34 34 35 35 36 36 37 37 38 38 39 39 40 43 44 Any help would be much appreciated! Cheers, Gal. ---
**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\ **Post date:** [October 14, 2021, 2:31pm UTC](https://ask.bioexcel.eu/t/pmx-problems-reproducing-benchmarking-from-de-groot-2020/3247/2 "2021-10-14T14:31:31Z")
The difference comes from using -alignment flag. I suggest trying to run the command without this flag: this way both MCS and alignment pathways in the script will be probed. The mapped atom pairs then should be the equivalent to those deposited on the pmx github repository (the ordering of the mapped pairs may be different, but it has no influence on the further steps). ---
**Author:** ![galmasrati](https://avatars.discourse-cdn.com/v4/letter/g/b9e5f3/32.png) [@galmasrati](https://ask.bioexcel.eu/u/galmasrati)\ **Post date:** [October 17, 2021, 5:15am UTC](https://ask.bioexcel.eu/t/pmx-problems-reproducing-benchmarking-from-de-groot-2020/3247/3 "2021-10-17T05:15:28Z")
Thanks Vytautas! I did as you suggested and it worked like a charm. Cheers, Gal.