# pmx **URL:** https://ask.bioexcel.eu/c/pmx/12.md?page=2 [Latest](https://ask.bioexcel.eu/latest.md) · [Categories](https://ask.bioexcel.eu/categories.md) · [Tags](https://ask.bioexcel.eu/tags.md) **Page:** 3 --- ## [Ligand topolgies for pmx](https://ask.bioexcel.eu/t/ligand-topolgies-for-pmx/3805)
**Author:** [@s.pallav](https://ask.bioexcel.eu/u/s.pallav)\ **Replies:** 5\ **Last updated:** [September 1, 2022, 1:10pm UTC](https://ask.bioexcel.eu/t/ligand-topolgies-for-pmx/3805 "2022-09-01T13:10:12Z")
Hello all, Can anyone give me an insight on the ffMOL.itp file which contains the (van der waals parameters) provided in the files in the Github page in Prot\_lig benchmark. How does one create such a file, I mean while … --- ## [Pmx RBFE gives oddly large deltaG](https://ask.bioexcel.eu/t/pmx-rbfe-gives-oddly-large-deltag/3847)
**Author:** [@k-zator](https://ask.bioexcel.eu/u/k-zator)\ **Replies:** 1\ **Last updated:** [August 14, 2022, 12:08pm UTC](https://ask.bioexcel.eu/t/pmx-rbfe-gives-oddly-large-deltag/3847 "2022-08-14T12:08:15Z")
Hello, I’m new to pmx still and have been trying to run RBFE for a macrocycle host and small molecule guests: glycine anhydride morphing into glycolide (hence NH → O). I’d like to believe the ligandHybrid step worked a… --- ## [PMX engineered resiude](https://ask.bioexcel.eu/t/pmx-engineered-resiude/3775)
**Author:** [@nandanhaloi123](https://ask.bioexcel.eu/u/nandanhaloi123)\ **Replies:** 4\ **Last updated:** [July 18, 2022, 8:04am UTC](https://ask.bioexcel.eu/t/pmx-engineered-resiude/3775 "2022-07-18T08:04:53Z")
Hello, I have a engineered residue (a chromophore) in my protein. I have the gromacs formated topology file for this and was trying to modify the library.py script of PMX but it seems very tedious and prone to mistake. … --- ## [Pmx ABFE ligand only simulation set-up](https://ask.bioexcel.eu/t/pmx-abfe-ligand-only-simulation-set-up/3800)
**Author:** [@k-zator](https://ask.bioexcel.eu/u/k-zator)\ **Replies:** 3\ **Last updated:** [July 18, 2022, 7:53am UTC](https://ask.bioexcel.eu/t/pmx-abfe-ligand-only-simulation-set-up/3800 "2022-07-18T07:53:40Z")
Hi, I’m trying to set up ABFE calculations for a guest-host system in water following the pmx abfe functionality. The complex works, although has some trouble minimising. I let it generate the guest-host constraints for… --- ## [Using pmx genlib and hybrid topologies](https://ask.bioexcel.eu/t/using-pmx-genlib-and-hybrid-topologies/3795)
**Author:** [@s.pallav](https://ask.bioexcel.eu/u/s.pallav)\ **Replies:** 3\ **Last updated:** [July 11, 2022, 6:46pm UTC](https://ask.bioexcel.eu/t/using-pmx-genlib-and-hybrid-topologies/3795 "2022-07-11T18:46:06Z")
Hello there, Is there anyway one can generate all the residues in mutres.mtp and mutres.rtp file of all the residues that are present in the force field including cgenff residues that are included in CHARMM36-Jul2021? … --- ## [PMX generating protein ligand simulation system with Charmm/cgenff forcefields](https://ask.bioexcel.eu/t/pmx-generating-protein-ligand-simulation-system-with-charmm-cgenff-forcefields/3657)
**Author:** [@mrinal\_shekhar](https://ask.bioexcel.eu/u/mrinal_shekhar)\ **Replies:** 1\ **Last updated:** [June 14, 2022, 3:21pm UTC](https://ask.bioexcel.eu/t/pmx-generating-protein-ligand-simulation-system-with-charmm-cgenff-forcefields/3657 "2022-06-14T15:21:39Z")
I am currently trying to replicate the Kinase resistance mutation work from Bert DeGroot lab using PMX . I am facing a bunch of errors in generating PMX gro files for the protein ligand system. I am following the followi… --- ## [Free energy calculations error](https://ask.bioexcel.eu/t/free-energy-calculations-error/3672)
**Author:** [@cyber222](https://ask.bioexcel.eu/u/cyber222)\ **Replies:** 1\ **Last updated:** [June 14, 2022, 3:17pm UTC](https://ask.bioexcel.eu/t/free-energy-calculations-error/3672 "2022-06-14T15:17:42Z")
Hello everyone, I am doing free energy calculations upon aminoacid mutation for the first time and got a problems. I want to calculate equilibrium trajectories for fast-growth method. Here is what I did. Downloaded PD… --- ## [Free Energy Calculation: State B has non-zero total charge: -1.000000](https://ask.bioexcel.eu/t/free-energy-calculation-state-b-has-non-zero-total-charge-1-000000/3738)
**Author:** [@sadafrani6](https://ask.bioexcel.eu/u/sadafrani6)\ **Replies:** 1\ **Last updated:** [June 14, 2022, 3:11pm UTC](https://ask.bioexcel.eu/t/free-energy-calculation-state-b-has-non-zero-total-charge-1-000000/3738 "2022-06-14T15:11:50Z")
Dear Bioexcel Community I need your suggestions regarding the following problem:- I am trying to calculate the free energy of mutating from Arginine to Histidine residue in a protein. I have prepared the system using p… --- ## [Free energy calculation with double system/single box simulation](https://ask.bioexcel.eu/t/free-energy-calculation-with-double-system-single-box-simulation/3478)
**Author:** [@almeida](https://ask.bioexcel.eu/u/almeida)\ **Replies:** 12\ **Last updated:** [March 30, 2022, 2:27pm UTC](https://ask.bioexcel.eu/t/free-energy-calculation-with-double-system-single-box-simulation/3478 "2022-03-30T14:27:24Z")
Hello, I want to calculate the relative binding free energy difference of a complex, with alchemical transformation using the double system/single box approach. I followed the tutorial on the pmx page (Mutation free ene… --- ## [Error with Zn atom](https://ask.bioexcel.eu/t/error-with-zn-atom/3599)
**Author:** [@almeida](https://ask.bioexcel.eu/u/almeida)\ **Replies:** 3\ **Last updated:** [March 29, 2022, 11:45am UTC](https://ask.bioexcel.eu/t/error-with-zn-atom/3599 "2022-03-29T11:45:48Z")
Hello, I am trying to prepare a DSSB system with pmx doublebox (Github package), but I get an error with a Zn atom. I have tried saving the pdb in several ways but still get this error: Traceback (most recent call last… --- ## [Problem with SS bridges - Bug?](https://ask.bioexcel.eu/t/problem-with-ss-bridges-bug/3574)
**Author:** [@almeida](https://ask.bioexcel.eu/u/almeida)\ **Replies:** 3\ **Last updated:** [March 24, 2022, 2:11pm UTC](https://ask.bioexcel.eu/t/problem-with-ss-bridges-bug/3574 "2022-03-24T14:11:25Z")
Hello, I am trying to set a system of a complex in which both host and ligand have 3 disulfide bridges. After the mutation with the server, only 1 bridge is retained in each chain in the output pdb. The input pdb has th… --- ## [Peptide Nucleic Acid Functionality](https://ask.bioexcel.eu/t/peptide-nucleic-acid-functionality/3353)
**Author:** [@Jack](https://ask.bioexcel.eu/u/Jack)\ **Replies:** 2\ **Last updated:** [January 2, 2022, 10:43am UTC](https://ask.bioexcel.eu/t/peptide-nucleic-acid-functionality/3353 "2022-01-02T10:43:32Z")
Hello, I use pmx a lot for free energy calculations - thanks for that! I was wondering if there are any plans to incorporate functionality to mutate peptide nucleic acid residues. I currently do so manually by copying … --- ## [Pmx - problems reproducing benchmarking from de Groot 2020](https://ask.bioexcel.eu/t/pmx-problems-reproducing-benchmarking-from-de-groot-2020/3247)
**Author:** [@galmasrati](https://ask.bioexcel.eu/u/galmasrati)\ **Replies:** 2\ **Last updated:** [October 17, 2021, 5:15am UTC](https://ask.bioexcel.eu/t/pmx-problems-reproducing-benchmarking-from-de-groot-2020/3247 "2021-10-17T05:15:28Z")
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 Gi… --- ## [Itp ligand file generation](https://ask.bioexcel.eu/t/itp-ligand-file-generation/2818)
**Author:** [@gian93](https://ask.bioexcel.eu/u/gian93)\ **Replies:** 3\ **Last updated:** [October 14, 2021, 2:34pm UTC](https://ask.bioexcel.eu/t/itp-ligand-file-generation/2818 "2021-10-14T14:34:59Z")
Dear all, In the pmx tutorial, it is described a workflow for thermodynamic integration of ligand. For the generation of the double topologies a gromacs file \*.itp is required: is there a way to write it? I previously p… --- ## [A non-finite potential energy in non-equilibrium transition with pmx](https://ask.bioexcel.eu/t/a-non-finite-potential-energy-in-non-equilibrium-transition-with-pmx/3141)
**Author:** [@QuocNgo](https://ask.bioexcel.eu/u/QuocNgo)\ **Replies:** 2\ **Last updated:** [October 1, 2021, 5:58pm UTC](https://ask.bioexcel.eu/t/a-non-finite-potential-energy-in-non-equilibrium-transition-with-pmx/3141 "2021-10-01T17:58:14Z")
I am carrying out an alchemical free energy calculations for amino acid mutation. When I performed non-equilibrium transition step, I had an issue. When I performed 50ps transition, the transition step worked perfectly w… --- ## [Alchemical free energy calculations](https://ask.bioexcel.eu/t/alchemical-free-energy-calculations/3102)
**Author:** [@isilayozturk](https://ask.bioexcel.eu/u/isilayozturk)\ **Replies:** 1\ **Last updated:** [October 1, 2021, 9:55am UTC](https://ask.bioexcel.eu/t/alchemical-free-energy-calculations/3102 "2021-10-01T09:55:19Z")
what is the main difference alchemical free energy calculations and umbrella or metadynamics ? --- ## [LINCS error during Alchemical free energy calculation](https://ask.bioexcel.eu/t/lincs-error-during-alchemical-free-energy-calculation/2904)
**Author:** [@rbhadane](https://ask.bioexcel.eu/u/rbhadane)\ **Replies:** 1\ **Last updated:** [September 30, 2021, 1:31pm UTC](https://ask.bioexcel.eu/t/lincs-error-during-alchemical-free-energy-calculation/2904 "2021-09-30T13:31:02Z")
I want to discuss the issue i am facing with pmx based free energy calculations. Briefly i have taken my protein which is in bound and unbound conformation, Then using pmx web-server i introduce one mutation (F2L) at po… --- ## [Energy minimization of hybrid ligand](https://ask.bioexcel.eu/t/energy-minimization-of-hybrid-ligand/2533)
**Author:** [@dburns](https://ask.bioexcel.eu/u/dburns)\ **Replies:** 2\ **Last updated:** [November 13, 2020, 2:48am UTC](https://ask.bioexcel.eu/t/energy-minimization-of-hybrid-ligand/2533 "2020-11-13T02:48:23Z")
Hello, I’ve got a hybrid ligand docked in the normal ligand binding site with no obvious steric clashes with surrounding residues. I cannot get the energy to minimize on one of the ligand atoms. Is this an issue that … --- ## [Dual Topology Generator for Alchemical Pathways](https://ask.bioexcel.eu/t/dual-topology-generator-for-alchemical-pathways/2043)
**Author:** [@jshmercado2556](https://ask.bioexcel.eu/u/jshmercado2556)\ **Replies:** 1\ **Last updated:** [October 9, 2020, 3:26pm UTC](https://ask.bioexcel.eu/t/dual-topology-generator-for-alchemical-pathways/2043 "2020-10-09T15:26:00Z")
I have a few questions regarding the online generator for Dual topologies for free energy calculations. Does this generator also include the use of a water model (tip3p)? If not, how would I account for this? I ask th… --- ## [Installed - can't import \_pmx as \_p](https://ask.bioexcel.eu/t/installed-cant-import-pmx-as-p/2290)
**Author:** [@dburns](https://ask.bioexcel.eu/u/dburns)\ **Replies:** 3\ **Last updated:** [July 4, 2020, 3:04pm UTC](https://ask.bioexcel.eu/t/installed-cant-import-pmx-as-p/2290 "2020-07-04T15:04:22Z")
I installed pmx on a cluster but was unable to get “pmx -h” to work. I get this error: Traceback (most recent call last): File “/home/dburns/.local/bin/pmx”, line 5, in from pmx.scripts.cli import entry\_point File … --- ## [Follow-Up from Webinar: Mutation free energy calculations with pmx](https://ask.bioexcel.eu/t/follow-up-from-webinar-mutation-free-energy-calculations-with-pmx/127)
**Author:** [@adamepcc](https://ask.bioexcel.eu/u/adamepcc)\ **Replies:** 0\ **Last updated:** [June 10, 2016, 2:50pm UTC](https://ask.bioexcel.eu/t/follow-up-from-webinar-mutation-free-energy-calculations-with-pmx/127 "2016-06-10T14:50:19Z")
Do you have any further questions relating to today's webinar on Mutation Free Energy Calculations with pmx? If so, please ask them in this thread, and our speakers will respond. [Previous page](https://ask.bioexcel.eu/c/pmx/12.md?page=1)