# pmx **URL:** https://ask.bioexcel.eu/c/pmx/12.md [Latest](https://ask.bioexcel.eu/latest.md) · [Categories](https://ask.bioexcel.eu/categories.md) · [Tags](https://ask.bioexcel.eu/tags.md) --- ## [About pmx: Automated protein structure and topology generation for alchemical perturbations](https://ask.bioexcel.eu/t/about-pmx-automated-protein-structure-and-topology-generation-for-alchemical-perturbations/126)
**Author:** [@rossen](https://ask.bioexcel.eu/u/rossen)\ **Replies:** 0
Automated protein structure and topology generation for alchemical perturbations. Web-server, source code, and examples at pmx.mpibpc.mpg.de/ . --- ## [Freezing previously-mutated residues in a staged/sequential multi-mutation pmx workflow](https://ask.bioexcel.eu/t/freezing-previously-mutated-residues-in-a-staged-sequential-multi-mutation-pmx-workflow/6264)
**Author:** [@Sankalp](https://ask.bioexcel.eu/u/Sankalp)\ **Replies:** 1\ **Last updated:** [September 17, 2026, 10:45am UTC](https://ask.bioexcel.eu/t/freezing-previously-mutated-residues-in-a-staged-sequential-multi-mutation-pmx-workflow/6264 "2026-09-17T10:45:28Z")
Hi all, I’m running a sequential (staged) multi-mutation alchemical calculation with pmx + GROMACS: I mutate one residue per stage (e.g. T2V), equilibrate both end states, then use the state-B equilibrated structure as … --- ## [RBFE for 8 simultaneous mutations](https://ask.bioexcel.eu/t/rbfe-for-8-simultaneous-mutations/6169)
**Author:** [@Sankalp](https://ask.bioexcel.eu/u/Sankalp)\ **Replies:** 6\ **Last updated:** [June 22, 2026, 7:28am UTC](https://ask.bioexcel.eu/t/rbfe-for-8-simultaneous-mutations/6169 "2026-06-22T07:28:58Z")
Hii, I have a beta-sheet protein of 128 residues, of which 8 are tyrosines. I have mutated all 8 TYR simultaneously to PHE. I used the same mdp files, except the temperature was changed to 300K. I followed the PMX prote… --- ## [NVT vs NPT for Non-Equilibrium Switching in pmx/GROMACS](https://ask.bioexcel.eu/t/nvt-vs-npt-for-non-equilibrium-switching-in-pmx-gromacs/5980)
**Author:** [@EidRashed](https://ask.bioexcel.eu/u/EidRashed)\ **Replies:** 1\ **Last updated:** [January 26, 2026, 11:19am UTC](https://ask.bioexcel.eu/t/nvt-vs-npt-for-non-equilibrium-switching-in-pmx-gromacs/5980 "2026-01-26T11:19:35Z")
I’m using pmx + GROMACS to run non-equilibrium alchemical free energy calculations for large protein–protein interactions (e.g., ~150 k atoms, like Fc–FcRn). My workflow is essentially: Equilibrate both end states (st… --- ## [Using PMX for ΔΔG on a glycosylated Fc (P238D back-mutation; PDB 3WJJ): viable workflows?](https://ask.bioexcel.eu/t/using-pmx-for-g-on-a-glycosylated-fc-p238d-back-mutation-pdb-3wjj-viable-workflows/5933)
**Author:** [@EidRashed](https://ask.bioexcel.eu/u/EidRashed)\ **Replies:** 5\ **Last updated:** [November 20, 2025, 3:29pm UTC](https://ask.bioexcel.eu/t/using-pmx-for-g-on-a-glycosylated-fc-p238d-back-mutation-pdb-3wjj-viable-workflows/5933 "2025-11-20T15:29:18Z")
Hi all, I’d like to use PMX to compute ΔΔG of binding for an Fc that is N-glycosylated (structure based on PDB: 3WJJ) by reversing the mutation P238D. I know PMX supports Amber and CHARMM family protein force fields out… --- ## [Absolute binding Free energy with NE-MD: Single-step complex leg & Boresch restraint tips](https://ask.bioexcel.eu/t/absolute-binding-free-energy-with-ne-md-single-step-complex-leg-boresch-restraint-tips/5840)
**Author:** [@ehsan](https://ask.bioexcel.eu/u/ehsan)\ **Replies:** 1\ **Last updated:** [August 4, 2025, 8:58am UTC](https://ask.bioexcel.eu/t/absolute-binding-free-energy-with-ne-md-single-step-complex-leg-boresch-restraint-tips/5840 "2025-08-04T08:58:51Z")
Hello PMX developers and users, I’m setting up an absolute binding free energy (ABFE) calculation using non-equilibrium MD with PMX/GROMACS, following the thermodynamic cycle (see attached image). Complex Leg (D → F) … --- ## [Issue in Probability distribution overlap for D2E transformation](https://ask.bioexcel.eu/t/issue-in-probability-distribution-overlap-for-d2e-transformation/5747)
**Author:** [@Vignesh\_SR](https://ask.bioexcel.eu/u/Vignesh_SR)\ **Replies:** 8\ **Last updated:** [July 4, 2025, 10:35am UTC](https://ask.bioexcel.eu/t/issue-in-probability-distribution-overlap-for-d2e-transformation/5747 "2025-07-04T10:35:36Z")
Dear All, I am performing amino acid transformation for my protein-peptide interaction studies. When I do D2E mutation in both peptide and complex arms with 51 lambdas (5 ns each), there is a poor Probability distribut… --- ## [Challenges in Reproducing ddG Estimation Results for 1STN](https://ask.bioexcel.eu/t/challenges-in-reproducing-ddg-estimation-results-for-1stn/4767)
**Author:** [@mstieffe](https://ask.bioexcel.eu/u/mstieffe)\ **Replies:** 28\ **Last updated:** [June 5, 2025, 9:30am UTC](https://ask.bioexcel.eu/t/challenges-in-reproducing-ddg-estimation-results-for-1stn/4767 "2025-06-05T09:30:39Z")
Hello, I am reaching out for assistance regarding an issue I encountered while attempting to reproduce the ddG estimation results for 1STN, as detailed in your paper, Accurate and Rigorous Prediction of the Changes in P… --- ## [Mutation free energy calculation for protein membrane interaction](https://ask.bioexcel.eu/t/mutation-free-energy-calculation-for-protein-membrane-interaction/5680)
**Author:** [@mac](https://ask.bioexcel.eu/u/mac)\ **Replies:** 2\ **Last updated:** [May 19, 2025, 8:03am UTC](https://ask.bioexcel.eu/t/mutation-free-energy-calculation-for-protein-membrane-interaction/5680 "2025-05-19T08:03:21Z")
Hi everyone! I wanted to know the effect of a mutation from Threonine to Serine on the interaction of a protein with a lipid bilayer, specifically in terms of energy change. I used the pmx tool to analyze the energy cha… --- ## [Repeatability of state A to State B alchemical transformation](https://ask.bioexcel.eu/t/repeatability-of-state-a-to-state-b-alchemical-transformation/5606)
**Author:** [@pinoji](https://ask.bioexcel.eu/u/pinoji)\ **Replies:** 2\ **Last updated:** [April 17, 2025, 1:44pm UTC](https://ask.bioexcel.eu/t/repeatability-of-state-a-to-state-b-alchemical-transformation/5606 "2025-04-17T13:44:04Z")
I am still new to this alchemical transformation. I have repeated same calculation 3 times for state A becoming state B. The results were DG=26 (4.2) kJ/mol, -2 (2.2) kJ/mol, and -4 (2.3) kJ/mol for the 1st run, 2nd ru… --- ## [PMX alchemical free energy calculation for protein mutation](https://ask.bioexcel.eu/t/pmx-alchemical-free-energy-calculation-for-protein-mutation/5537)
**Author:** [@rakibpharma](https://ask.bioexcel.eu/u/rakibpharma)\ **Replies:** 1\ **Last updated:** [March 25, 2025, 12:34pm UTC](https://ask.bioexcel.eu/t/pmx-alchemical-free-energy-calculation-for-protein-mutation/5537 "2025-03-25T12:34:49Z")
I am trying to reproduce the results ΔΔG of protein mutation (W6F), that you have provided in Protein mutation — pmx documentation. I have used devlop branch of pmx for alchemical calculation. I am using the parameters … --- ## [Pmx ligandHybrid error](https://ask.bioexcel.eu/t/pmx-ligandhybrid-error/5441)
**Author:** [@mukherjee175](https://ask.bioexcel.eu/u/mukherjee175)\ **Replies:** 7\ **Last updated:** [March 15, 2025, 3:26pm UTC](https://ask.bioexcel.eu/t/pmx-ligandhybrid-error/5441 "2025-03-15T15:26:33Z")
Hi, I was hoping to perform RBFE calculations where I change Phenylalanine (PHE) to an unnatural amino acid 2-methylPhenylalanine(MPH2) using CharmmFF. The mutations supported by pmx are all natural amino acids. I searc… --- ## [PMX Ligand Preparation from Scratch - Atom Types and Parameter Discrepancies](https://ask.bioexcel.eu/t/pmx-ligand-preparation-from-scratch-atom-types-and-parameter-discrepancies/5429)
**Author:** [@jinurajkr](https://ask.bioexcel.eu/u/jinurajkr)\ **Replies:** 2\ **Last updated:** [February 28, 2025, 11:49am UTC](https://ask.bioexcel.eu/t/pmx-ligand-preparation-from-scratch-atom-types-and-parameter-discrepancies/5429 "2025-02-28T11:49:21Z")
Dear All We are writing to you regarding the preparation of ligands from scratch for running in PMX. We obtained the SDF file for the ligand from the following reference: \[https://pubs.acs.org/doi/10.1021/ja512751q\] Ou… --- ## [Error with pmx and openforcefield generated files](https://ask.bioexcel.eu/t/error-with-pmx-and-openforcefield-generated-files/5402)
**Author:** [@lwhitm1](https://ask.bioexcel.eu/u/lwhitm1)\ **Replies:** 1\ **Last updated:** [January 27, 2025, 11:46am UTC](https://ask.bioexcel.eu/t/error-with-pmx-and-openforcefield-generated-files/5402 "2025-01-27T11:46:05Z")
I have attempted to use openff-toolkit generate files as inputs for the ligand\_tutorial. The atomMapping finished without error, but, during the makeHybrid component, I get this error in my log file: " ligandHybridTop… --- ## [Pmx and CHARM36 using output from CGenFF server](https://ask.bioexcel.eu/t/pmx-and-charm36-using-output-from-cgenff-server/5397)
**Author:** [@pinoji](https://ask.bioexcel.eu/u/pinoji)\ **Replies:** 3\ **Last updated:** [January 20, 2025, 9:12am UTC](https://ask.bioexcel.eu/t/pmx-and-charm36-using-output-from-cgenff-server/5397 "2025-01-20T09:12:45Z")
Is the PMX compatible with CHARM36 output I get from CGenFF server? The output folder contains mol2, err, and str. The other GROMACS output folder contains pdb, and top file along with ff related files. Am I suppose t… --- ## [Pmx analyse says "no good dgdl files provided"](https://ask.bioexcel.eu/t/pmx-analyse-says-no-good-dgdl-files-provided/5394)
**Author:** [@mukherjee175](https://ask.bioexcel.eu/u/mukherjee175)\ **Replies:** 2\ **Last updated:** [January 13, 2025, 3:58pm UTC](https://ask.bioexcel.eu/t/pmx-analyse-says-no-good-dgdl-files-provided/5394 "2025-01-13T15:58:27Z")
I am working with a protein-peptide complex. I aim to do mutations on the peptide. I was performing mutation free energy calculations using the Fast growth method following the tutorial of the Trp cage. When I use pmx an… --- ## [Installation Problem of PMX](https://ask.bioexcel.eu/t/installation-problem-of-pmx/5323)
**Author:** [@vnbalaji](https://ask.bioexcel.eu/u/vnbalaji)\ **Replies:** 12\ **Last updated:** [January 13, 2025, 9:45am UTC](https://ask.bioexcel.eu/t/installation-problem-of-pmx/5323 "2025-01-13T09:45:45Z")
I am encountering the following error during installation of pmx in conda. Please suggest solution. Thanks. Balaji. Requirement already satisfied: six\>=1.5 in c:\\programdata\\anaconda3\\envs\\pmx\\lib\\site-packages (from pyt… --- ## [Help request protein-ligand tutorial error fix](https://ask.bioexcel.eu/t/help-request-protein-ligand-tutorial-error-fix/5353)
**Author:** [@vnbalaji](https://ask.bioexcel.eu/u/vnbalaji)\ **Replies:** 8\ **Last updated:** [December 30, 2024, 11:42am UTC](https://ask.bioexcel.eu/t/help-request-protein-ligand-tutorial-error-fix/5353 "2024-12-30T11:42:28Z")
Request help to fix this in some detail. I was following the tutorial: ligand\_tutorial At the step doing eq\_nvt, I believe I am encountering two errors. I do not know how to fix this and move forward. I am enclosing t… --- ## [Help with Charged Ligand Non-Equilibrium Free Energy Calculations Using Co-Alchemical Ion Approach](https://ask.bioexcel.eu/t/help-with-charged-ligand-non-equilibrium-free-energy-calculations-using-co-alchemical-ion-approach/5371)
**Author:** [@mpapadourakis](https://ask.bioexcel.eu/u/mpapadourakis)\ **Replies:** 3\ **Last updated:** [December 20, 2024, 12:48pm UTC](https://ask.bioexcel.eu/t/help-with-charged-ligand-non-equilibrium-free-energy-calculations-using-co-alchemical-ion-approach/5371 "2024-12-20T12:48:40Z")
Hi everyone, I’m working on free energy calculations for a charged ligand (+1) bound to a protein. As I’m new to handling charge-changing perturbations, I would appreciate some guidance. I attempted the co-alchemical i… --- ## [Relative constraint deviation after LINCS](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496)
**Author:** [@dburns](https://ask.bioexcel.eu/u/dburns)\ **Replies:** 15\ **Last updated:** [December 9, 2024, 11:13am UTC](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496 "2024-12-09T11:13:56Z")
Hello, I’m using the eqA.mdp file from the tutorial here: Despite running several equilibration steps with and without restraints on my ligand I get the error: Step 3, time 0.006 (ps) LINCS WARNING relative cons… --- ## [LINCS warning and segmentation fault @ non-equilibrium part of simulation](https://ask.bioexcel.eu/t/lincs-warning-and-segmentation-fault-non-equilibrium-part-of-simulation/5352)
**Author:** [@tkoh](https://ask.bioexcel.eu/u/tkoh)\ **Replies:** 7\ **Last updated:** [December 9, 2024, 8:12am UTC](https://ask.bioexcel.eu/t/lincs-warning-and-segmentation-fault-non-equilibrium-part-of-simulation/5352 "2024-12-09T08:12:00Z")
Hi everyone, So I am trying to do free energy calculations for a mutant (M205A) with the human Prion protein (1QLX). However I keep running into a lincs warning at the non equilirium phase of the free energy simulation.… --- ## [PMX AssertionError, Atom type OH not been defined in the force field, Atom DHD1 was not found](https://ask.bioexcel.eu/t/pmx-assertionerror-atom-type-oh-not-been-defined-in-the-force-field-atom-dhd1-was-not-found/5332)
**Author:** [@genetics](https://ask.bioexcel.eu/u/genetics)\ **Replies:** 3\ **Last updated:** [November 13, 2024, 8:57am UTC](https://ask.bioexcel.eu/t/pmx-assertionerror-atom-type-oh-not-been-defined-in-the-force-field-atom-dhd1-was-not-found/5332 "2024-11-13T08:57:57Z")
I am using developmental version of PMX. Python 3.11.0. Gromacs version 2024.4. I am trying to mutate 276 residue from R2W. My WT.pdb file has total 320 aa. head WT.pdb ATOM 1 N MET A 1 -23.707 -0.652 1… --- ## [After running the ddG calculation tutorial (ligand\_tutorial.ipynb), I got different result](https://ask.bioexcel.eu/t/after-running-the-ddg-calculation-tutorial-ligand-tutorial-ipynb-i-got-different-result/5302)
**Author:** [@soymilk](https://ask.bioexcel.eu/u/soymilk)\ **Replies:** 7\ **Last updated:** [October 28, 2024, 8:05am UTC](https://ask.bioexcel.eu/t/after-running-the-ddg-calculation-tutorial-ligand-tutorial-ipynb-i-got-different-result/5302 "2024-10-28T08:05:53Z")
Hello, I practiced calculating ddG using the ligand\_tutorial.ipynb from the pmx (developer) branch. In the tutorial, the expected result is -3.2 kJ/mol, and the example result on GitHub shows a similar value of -3.0 kJ/… --- ## [Non-standard amino acid mutation - dihedrals error](https://ask.bioexcel.eu/t/non-standard-amino-acid-mutation-dihedrals-error/5257)
**Author:** [@Vignesh\_SR](https://ask.bioexcel.eu/u/Vignesh_SR)\ **Replies:** 2\ **Last updated:** [September 25, 2024, 12:37pm UTC](https://ask.bioexcel.eu/t/non-standard-amino-acid-mutation-dihedrals-error/5257 "2024-09-25T12:37:13Z")
Dear All, I am working on amino acid mutations and I found an interesting opportunity to mutate Arginine to Homoarginine for my study. I made mutres.mtp and mutres.rtp for this mutation (R2Z) , based on the available da… --- ## [Is the pmx web-server OK?](https://ask.bioexcel.eu/t/is-the-pmx-web-server-ok/5267)
**Author:** [@burunduk](https://ask.bioexcel.eu/u/burunduk)\ **Replies:** 1\ **Last updated:** [September 25, 2024, 7:19am UTC](https://ask.bioexcel.eu/t/is-the-pmx-web-server-ok/5267 "2024-09-25T07:19:50Z")
HiDear PMX server developers, Since yesterday the server is available only through http, not https, as I used it previously. I subbmitted few tasks, but they are not ready yet, while previously it was just couple of mi… --- ## [Pmx and protein structure water molecules](https://ask.bioexcel.eu/t/pmx-and-protein-structure-water-molecules/5041)
**Author:** [@raitis.bobrovs](https://ask.bioexcel.eu/u/raitis.bobrovs)\ **Replies:** 2\ **Last updated:** [May 24, 2024, 1:06pm UTC](https://ask.bioexcel.eu/t/pmx-and-protein-structure-water-molecules/5041 "2024-05-24T13:06:28Z")
Hi, all I am having some problems with pmx when I want to use it with my protein structure that also contains water molecules. Everything did run fine when I tried to set up and run the system without co-crystallised w… --- ## [Error in AtomMapping with more than 100 atoms](https://ask.bioexcel.eu/t/error-in-atommapping-with-more-than-100-atoms/4903)
**Author:** [@AngelicaSandoval](https://ask.bioexcel.eu/u/AngelicaSandoval)\ **Replies:** 2\ **Last updated:** [April 4, 2024, 4:57pm UTC](https://ask.bioexcel.eu/t/error-in-atommapping-with-more-than-100-atoms/4903 "2024-04-04T16:57:19Z")
Hi everyone I am trying to use the pmx atomMapping, to create a hybrid topology for ligands. Whenever I try to do the mapping with more than 100 atoms (including hydrogens) it fails and shows the following error: Canno… --- ## [Pmx error pmx mutate -f protein.pdb -o mutant.pdb](https://ask.bioexcel.eu/t/pmx-error-pmx-mutate-f-protein-pdb-o-mutant-pdb/4869)
**Author:** [@marichi](https://ask.bioexcel.eu/u/marichi)\ **Replies:** 1\ **Last updated:** [March 6, 2024, 7:04am UTC](https://ask.bioexcel.eu/t/pmx-error-pmx-mutate-f-protein-pdb-o-mutant-pdb/4869 "2024-03-06T07:04:12Z")
I hope this message finds you well. I am currently working with the pmx mutate command in the PMX tool, attempting to prepare hybrid files by mutating residues in a protein structure. I am also aware that for this step I… --- ## ['ligandHybrid' ERROR: fitting mol2 on mol1 failed](https://ask.bioexcel.eu/t/ligandhybrid-error-fitting-mol2-on-mol1-failed/4846)
**Author:** [@yehon](https://ask.bioexcel.eu/u/yehon)\ **Replies:** 4\ **Last updated:** [February 21, 2024, 9:53am UTC](https://ask.bioexcel.eu/t/ligandhybrid-error-fitting-mol2-on-mol1-failed/4846 "2024-02-21T09:53:47Z")
Hello, I’ve been working on merging itp files for my ligands using the ‘ligandHybrid’ script, but I’m encountering issues with specific ligands. While the tool works fine for some, others result in errors during the hybr… --- ## [LINCS constraints all bonds to h-bonds only](https://ask.bioexcel.eu/t/lincs-constraints-all-bonds-to-h-bonds-only/4839)
**Author:** [@obeyens](https://ask.bioexcel.eu/u/obeyens)\ **Replies:** 7\ **Last updated:** [February 16, 2024, 2:43pm UTC](https://ask.bioexcel.eu/t/lincs-constraints-all-bonds-to-h-bonds-only/4839 "2024-02-16T14:43:58Z")
Hi everyone, In the mdp files on the github pages of pmx benchmarks, LINCS constraints are always set to ‘all-bonds’. However, this causes a significant hit in performance on GPUs as the -update gpu flag to mdrun cannot… [Next page](https://ask.bioexcel.eu/c/pmx/12.md?page=1)