# pmx **URL:** https://ask.bioexcel.eu/c/pmx/12.md?page=1 [Latest](https://ask.bioexcel.eu/latest.md) · [Categories](https://ask.bioexcel.eu/categories.md) · [Tags](https://ask.bioexcel.eu/tags.md) **Page:** 2 --- ## [Error with 'make\_hybrid.py' Using CGenFF](https://ask.bioexcel.eu/t/error-with-make-hybrid-py-using-cgenff/4820)
**Author:** [@yehon](https://ask.bioexcel.eu/u/yehon)\ **Replies:** 4\ **Last updated:** [February 12, 2024, 1:12pm UTC](https://ask.bioexcel.eu/t/error-with-make-hybrid-py-using-cgenff/4820 "2024-02-12T13:12:17Z")
Hello to all, I encountered an error while attempting to execute ‘make\_hybrid.py’: Traceback (most recent call last): File “…/scripts/ligands/make\_hybrid.py”, line 1308, in main( sys.argv ) File “…/scripts/ligands/… --- ## [Issue with pdb2gmx and charm36mut forcefield: Undefined Atom Type "OH"](https://ask.bioexcel.eu/t/issue-with-pdb2gmx-and-charm36mut-forcefield-undefined-atom-type-oh/4671)
**Author:** [@mstieffe](https://ask.bioexcel.eu/u/mstieffe)\ **Replies:** 4\ **Last updated:** [December 7, 2023, 1:04pm UTC](https://ask.bioexcel.eu/t/issue-with-pdb2gmx-and-charm36mut-forcefield-undefined-atom-type-oh/4671 "2023-12-07T13:04:11Z")
Hello everyone, I am encountering an issue when using pdb2gmx with the charm36mut forcefield. The error message I receive is: “Atom type OH specified in terminal database has not been defined in the force field.” I have… --- ## [Make\_hybrid.py list index out of range error](https://ask.bioexcel.eu/t/make-hybrid-py-list-index-out-of-range-error/2488)
**Author:** [@dburns](https://ask.bioexcel.eu/u/dburns)\ **Replies:** 14\ **Last updated:** [December 4, 2023, 11:35pm UTC](https://ask.bioexcel.eu/t/make-hybrid-py-list-index-out-of-range-error/2488 "2023-12-04T23:35:03Z")
Hi, Could someone suggest where my problem is coming from with the following output from make\_hybrid.py? I’m using the charmm36 forcefield and following the latest ligand tutorial. My only commands to this point: ato… --- ## [Questions on Non-equilibrium TI Phase with Slurm Scheduler in 'AZtutorial.py' Script](https://ask.bioexcel.eu/t/questions-on-non-equilibrium-ti-phase-with-slurm-scheduler-in-aztutorial-py-script/4689)
**Author:** [@jungyong](https://ask.bioexcel.eu/u/jungyong)\ **Replies:** 2\ **Last updated:** [December 4, 2023, 9:37am UTC](https://ask.bioexcel.eu/t/questions-on-non-equilibrium-ti-phase-with-slurm-scheduler-in-aztutorial-py-script/4689 "2023-12-04T09:37:40Z")
Hello PMX community, I have been using a customized ‘AZtutorial.py’ script from the tutorial, and I’ve come across a few questions related to non-equilibrium TI phase calculations with the Slurm scheduler. Absence of … --- ## [Error using mutate.py with charmm FF](https://ask.bioexcel.eu/t/error-using-mutate-py-with-charmm-ff/4663)
**Author:** [@mstieffe](https://ask.bioexcel.eu/u/mstieffe)\ **Replies:** 3\ **Last updated:** [December 1, 2023, 4:40pm UTC](https://ask.bioexcel.eu/t/error-using-mutate-py-with-charmm-ff/4663 "2023-12-01T16:40:42Z")
Hello, I experience some issues while going through your tutorial for mutation free energies. When I run the mutate.py command with the amber or opls FF everything works fine. However, when i select one of the charmm FF… --- ## [Mutation involving two proteins](https://ask.bioexcel.eu/t/mutation-involving-two-proteins/4707)
**Author:** [@pinoji](https://ask.bioexcel.eu/u/pinoji)\ **Replies:** 2\ **Last updated:** [November 29, 2023, 7:42pm UTC](https://ask.bioexcel.eu/t/mutation-involving-two-proteins/4707 "2023-11-29T19:42:44Z")
Is there a way to mutate x residue in Chain\_A (1000atoms) and y residue in Chain\_B(2000atoms) using pmx? I tried to submit one to webpmx but it did not accept. If not, do I just add all whole numbers assigned for atoms… --- ## [Performing Non-equilibrium Alchemical Transformations with Multiple Mutations](https://ask.bioexcel.eu/t/performing-non-equilibrium-alchemical-transformations-with-multiple-mutations/4695)
**Author:** [@mstieffe](https://ask.bioexcel.eu/u/mstieffe)\ **Replies:** 3\ **Last updated:** [November 24, 2023, 12:21pm UTC](https://ask.bioexcel.eu/t/performing-non-equilibrium-alchemical-transformations-with-multiple-mutations/4695 "2023-11-24T12:21:52Z")
Hello everyone, I am currently working on non-equilibrium alchemical transformation simulations involving multiple residue mutations, which may include several charge changes. I am aware of the “two systems in a single … --- ## [Please help me understand these values from the tutorial](https://ask.bioexcel.eu/t/please-help-me-understand-these-values-from-the-tutorial/4664)
**Author:** [@mstieffe](https://ask.bioexcel.eu/u/mstieffe)\ **Replies:** 4\ **Last updated:** [November 23, 2023, 2:27pm UTC](https://ask.bioexcel.eu/t/please-help-me-understand-these-values-from-the-tutorial/4664 "2023-11-23T14:27:27Z")
Hello, I am having a hard time understanding the dG and ddG values that I obtain when going through the amino acid mutation tutorial. I downloaded the dhdl files for the slow growth. Is this slow growth approach what… --- ## [Theoretical question about 'one box two systems'](https://ask.bioexcel.eu/t/theoretical-question-about-one-box-two-systems/4678)
**Author:** [@obeyens](https://ask.bioexcel.eu/u/obeyens)\ **Replies:** 4\ **Last updated:** [November 22, 2023, 10:06am UTC](https://ask.bioexcel.eu/t/theoretical-question-about-one-box-two-systems/4678 "2023-11-22T10:06:09Z")
Hello everyone, I am planning on doing some ligand relative binding free energy calculations using pmx that involve charged mutations. The recommended protocol seems ‘one box two systems’. If I apply this to my problem,… --- ## [PMX protein mutation tutorial](https://ask.bioexcel.eu/t/pmx-protein-mutation-tutorial/4656)
**Author:** [@pinoji](https://ask.bioexcel.eu/u/pinoji)\ **Replies:** 6\ **Last updated:** [November 10, 2023, 8:44am UTC](https://ask.bioexcel.eu/t/pmx-protein-mutation-tutorial/4656 "2023-11-10T08:44:53Z")
I am trying to follow this tutorial. https://degrootlab.github.io/pmx/tutorials/protein\_mut.html After all computations up to Non-equilibrium MD are done, I got this plot. I repeated the same calculations and got ve… --- ## [Different masses of dummy atoms in webserver pmx and standalone pmx](https://ask.bioexcel.eu/t/different-masses-of-dummy-atoms-in-webserver-pmx-and-standalone-pmx/4612)
**Author:** [@Mary](https://ask.bioexcel.eu/u/Mary)\ **Replies:** 1\ **Last updated:** [October 31, 2023, 9:08am UTC](https://ask.bioexcel.eu/t/different-masses-of-dummy-atoms-in-webserver-pmx-and-standalone-pmx/4612 "2023-10-31T09:08:27Z")
Dear Gromacs users, I am trying to calculate ddG of folding of barnase mutant H18D (barnase ID: 1BNI) using FEP with double system/single box protocol. While generating hybrid structures for barnase and tripeptide I not… --- ## [The use of GAFF1 vs GAFF2 with the pmx ff99SB\*-ILDN forcefield](https://ask.bioexcel.eu/t/the-use-of-gaff1-vs-gaff2-with-the-pmx-ff99sb-ildn-forcefield/4628)
**Author:** [@obeyens](https://ask.bioexcel.eu/u/obeyens)\ **Replies:** 2\ **Last updated:** [October 25, 2023, 1:37pm UTC](https://ask.bioexcel.eu/t/the-use-of-gaff1-vs-gaff2-with-the-pmx-ff99sb-ildn-forcefield/4628 "2023-10-25T13:37:45Z")
Hello everyone, I have found some conflicting indications in literature on the recommended GAFF version for use with the modified Amber99sb\*ILDN force field shipped with PMX. The 2019 article ‘Large scale relative prot… --- ## [Pmx webserver is not running](https://ask.bioexcel.eu/t/pmx-webserver-is-not-running/4613)
**Author:** [@Mary](https://ask.bioexcel.eu/u/Mary)\ **Replies:** 1\ **Last updated:** [October 18, 2023, 3:38pm UTC](https://ask.bioexcel.eu/t/pmx-webserver-is-not-running/4613 "2023-10-18T15:38:34Z")
Hello! I am trying to create a hybrid topology for my protein in webserver version of pmx, but my job has been in the queue since last week. There was no update on the website since 2022. Is it still working? Thank yo… --- ## [Help Needed with Protein-Ligand Topology in pmx Tutorial](https://ask.bioexcel.eu/t/help-needed-with-protein-ligand-topology-in-pmx-tutorial/4598)
**Author:** [@jungyong](https://ask.bioexcel.eu/u/jungyong)\ **Replies:** 4\ **Last updated:** [October 13, 2023, 9:25am UTC](https://ask.bioexcel.eu/t/help-needed-with-protein-ligand-topology-in-pmx-tutorial/4598 "2023-10-13T09:25:46Z")
Hello! I’m seeking assistance. I plan to process the protein and ligand to use them as input for the pmx tutorial. As mentioned in the following URL: I have created topology using pdb2gmx and acpype+anteamber with t… --- ## [Problem with installing with Python2](https://ask.bioexcel.eu/t/problem-with-installing-with-python2/3885)
**Author:** [@s.pallav](https://ask.bioexcel.eu/u/s.pallav)\ **Replies:** 10\ **Last updated:** [October 13, 2023, 7:22am UTC](https://ask.bioexcel.eu/t/problem-with-installing-with-python2/3885 "2023-10-13T07:22:32Z")
Dear all, I am encountering problem with installing pmx with Python2.7 which has a problem with matplotlib version. Has anyone come across such sort of problem? I wanted to use the scripts from the master branch particu… --- ## [Pmx ligandHybrid list index out of range error](https://ask.bioexcel.eu/t/pmx-ligandhybrid-list-index-out-of-range-error/4413)
**Author:** [@limmski](https://ask.bioexcel.eu/u/limmski)\ **Replies:** 4\ **Last updated:** [July 19, 2023, 12:55pm UTC](https://ask.bioexcel.eu/t/pmx-ligandhybrid-list-index-out-of-range-error/4413 "2023-07-19T12:55:50Z")
Hello, I am currently using pmx to create hybrid topologies and ran into an list index error: IndexError: list index out of range I used ligandHybrid from pmx: pmx ligandHybrid -i1 t1.pdb -i2 t2.pdb -itp1 t1.itp -itp… --- ## [Absolute Binding Free Energy with pmx](https://ask.bioexcel.eu/t/absolute-binding-free-energy-with-pmx/4313)
**Author:** [@AndreaSaltalamacchia](https://ask.bioexcel.eu/u/AndreaSaltalamacchia)\ **Replies:** 5\ **Last updated:** [May 24, 2023, 11:50am UTC](https://ask.bioexcel.eu/t/absolute-binding-free-energy-with-pmx/4313 "2023-05-24T11:50:47Z")
Hi everybody, I was trying to find some tutorial on pmx to compute ligand absolute binding free energy, however I could only find a lot of tutorial for RELATIVE free energy. Do you know any practical resources that I c… --- ## [PMX user survey](https://ask.bioexcel.eu/t/pmx-user-survey/4343)
**Author:** [@bgroot](https://ask.bioexcel.eu/u/bgroot)\ **Replies:** 0\ **Last updated:** [May 23, 2023, 2:49pm UTC](https://ask.bioexcel.eu/t/pmx-user-survey/4343 "2023-05-23T14:49:42Z")
Dear PMX users and enthusiasts of alchemical free energy calculations, please take a moment of your time to fill out this PMX survey to help us prioritize your suggestions for PMX improvements and development. Thank you … --- ## [PMX tutorial free energy sign](https://ask.bioexcel.eu/t/pmx-tutorial-free-energy-sign/4309)
**Author:** [@Hryhory\_Sinenka](https://ask.bioexcel.eu/u/Hryhory_Sinenka)\ **Replies:** 1\ **Last updated:** [May 11, 2023, 12:27pm UTC](https://ask.bioexcel.eu/t/pmx-tutorial-free-energy-sign/4309 "2023-05-11T12:27:39Z")
Dear Dr. Gapsys, This is a very simple question, just to resolve some possible misinterpretations. In the 2020 Tutorial (Ligand modification free energy calculations) in the very end there is a phrase “The calculated v… --- ## [Pmx: possibility to run only once the dynamics of state A for A-\>B and A-\>C transformations + small question on the sign of dG](https://ask.bioexcel.eu/t/pmx-possibility-to-run-only-once-the-dynamics-of-state-a-for-a-b-and-a-c-transformations-small-question-on-the-sign-of-dg/4270)
**Author:** [@Hryhory\_Sinenka](https://ask.bioexcel.eu/u/Hryhory_Sinenka)\ **Replies:** 5\ **Last updated:** [May 1, 2023, 8:59am UTC](https://ask.bioexcel.eu/t/pmx-possibility-to-run-only-once-the-dynamics-of-state-a-for-a-b-and-a-c-transformations-small-question-on-the-sign-of-dg/4270 "2023-05-01T08:59:09Z")
Dear Dr. Gapsys, Thank you very much for the pmx tool, it looks very promising to use for my PhD research! I would be very grateful if you could help me with two interconnected questions (and one auxiliary): For me i… --- ## [Is the pmx server running?](https://ask.bioexcel.eu/t/is-the-pmx-server-running/4264)
**Author:** [@nori](https://ask.bioexcel.eu/u/nori)\ **Replies:** 2\ **Last updated:** [April 17, 2023, 6:22am UTC](https://ask.bioexcel.eu/t/is-the-pmx-server-running/4264 "2023-04-17T06:22:31Z")
Thank you very much for sharing the excellent tool. Is the pmx protein web server running now? It worked well earlier this month, but does not these days for me. Nothing happens after ‘Your jobs is still in the queue/run… --- ## [PMX repeatability is very poor](https://ask.bioexcel.eu/t/pmx-repeatability-is-very-poor/4234)
**Author:** [@lyh](https://ask.bioexcel.eu/u/lyh)\ **Replies:** 8\ **Last updated:** [April 4, 2023, 7:36am UTC](https://ask.bioexcel.eu/t/pmx-repeatability-is-very-poor/4234 "2023-04-04T07:36:15Z")
Dear Bioexcel users, I use PMX to calculate when Ser mutates into Phe, when calculating ΔG in water, the repeatability is very poor, I use the version of gromacs2020.7. In addition, I would like to ask if the trajector… --- ## [Janssen Ligand tutorial: why no -H2Hpolar flag in atoms\_to\_morph.py?](https://ask.bioexcel.eu/t/janssen-ligand-tutorial-why-no-h2hpolar-flag-in-atoms-to-morph-py/4210)
**Author:** [@obeyens](https://ask.bioexcel.eu/u/obeyens)\ **Replies:** 1\ **Last updated:** [March 22, 2023, 12:32pm UTC](https://ask.bioexcel.eu/t/janssen-ligand-tutorial-why-no-h2hpolar-flag-in-atoms-to-morph-py/4210 "2023-03-22T12:32:58Z")
Dear all, I am doing the Janssen ligand tutorial: Ligand modification free energy calculations. During the atom mapping step using atoms\_to\_morph.py the following command is used: $ python atoms\_to\_morph.py -i1 lig\_1a… --- ## [AMBER99SB-ILDN warning alert](https://ask.bioexcel.eu/t/amber99sb-ildn-warning-alert/4135)
**Author:** [@Brijesh](https://ask.bioexcel.eu/u/Brijesh)\ **Replies:** 3\ **Last updated:** [March 10, 2023, 8:43am UTC](https://ask.bioexcel.eu/t/amber99sb-ildn-warning-alert/4135 "2023-03-10T08:43:41Z")
Dear Bioexcel users, I am using the AMBER99SB-ILDN force field for simulation. While using pdb2gmx, I get a warning WARNING: Duplicate line found in or between hackblock and rtp entries. I don’t get this warning while … --- ## [Understanding the options of atom mapping and ligandHybrid](https://ask.bioexcel.eu/t/understanding-the-options-of-atom-mapping-and-ligandhybrid/4023)
**Author:** [@s.pallav](https://ask.bioexcel.eu/u/s.pallav)\ **Replies:** 57\ **Last updated:** [February 23, 2023, 12:07pm UTC](https://ask.bioexcel.eu/t/understanding-the-options-of-atom-mapping-and-ligandhybrid/4023 "2023-02-23T12:07:17Z")
Dear users and developers, How do atom mapping options for ligand RBFE differ from each other as in where I use (–H2Heavy option, whether hydrogen be morphed into a heavy atom) and I have been unable to get forward and … --- ## [Oscillational period warning during tripeptide A2I forward simulation](https://ask.bioexcel.eu/t/oscillational-period-warning-during-tripeptide-a2i-forward-simulation/4034)
**Author:** [@jasoank](https://ask.bioexcel.eu/u/jasoank)\ **Replies:** 14\ **Last updated:** [January 31, 2023, 11:49am UTC](https://ask.bioexcel.eu/t/oscillational-period-warning-during-tripeptide-a2i-forward-simulation/4034 "2023-01-31T11:49:15Z")
Hello, I’m trying to perform forward and reverse simulations for Mutation free energy calculations. I have successfully calculated the total ddG of several tripeptides. They output similar ddG values to pmx webserver. Ho… --- ## [Problem in using gentop](https://ask.bioexcel.eu/t/problem-in-using-gentop/4073)
**Author:** [@s.pallav](https://ask.bioexcel.eu/u/s.pallav)\ **Replies:** 12\ **Last updated:** [January 20, 2023, 5:01am UTC](https://ask.bioexcel.eu/t/problem-in-using-gentop/4073 "2023-01-20T05:01:52Z")
Hi @vgapsys, I have been trying my hand in protein mutations and while using the pmx gentop to fill in the B states I have been encountering an error like this: pmx gentop -f topol.top -o newtop.top -ff ./mutff45/charm… --- ## [List index out of range when running pmx gentop](https://ask.bioexcel.eu/t/list-index-out-of-range-when-running-pmx-gentop/4049)
**Author:** [@Alfredo](https://ask.bioexcel.eu/u/Alfredo)\ **Replies:** 2\ **Last updated:** [December 29, 2022, 4:15pm UTC](https://ask.bioexcel.eu/t/list-index-out-of-range-when-running-pmx-gentop/4049 "2022-12-29T16:15:15Z")
Hi, I am new using pmx. I am using python3.7 so I loaded the develop version. I am trying to mutate the first amino acid of a 24-AA peptide from F → A. I am running in the command line. I used: pmx mutate -f naf1\_fromc… --- ## [Bonds that rotated more than 30 degrees:](https://ask.bioexcel.eu/t/bonds-that-rotated-more-than-30-degrees/3944)
**Author:** [@yang1](https://ask.bioexcel.eu/u/yang1)\ **Replies:** 1\ **Last updated:** [November 3, 2022, 1:31pm UTC](https://ask.bioexcel.eu/t/bonds-that-rotated-more-than-30-degrees/3944 "2022-11-03T13:31:37Z")
hi , all when I have using the pmx run the moleculer dynamics, I have some trouble in my process. I have done the NVT and NPT , when I have begain my production steps, the wrong have appeared. Step 27126, time 54.252 … --- ## [IndexError: list index out of range while preparing pdb file](https://ask.bioexcel.eu/t/indexerror-list-index-out-of-range-while-preparing-pdb-file/3904)
**Author:** [@Brijesh](https://ask.bioexcel.eu/u/Brijesh)\ **Replies:** 1\ **Last updated:** [September 15, 2022, 9:38am UTC](https://ask.bioexcel.eu/t/indexerror-list-index-out-of-range-while-preparing-pdb-file/3904 "2022-09-15T09:38:19Z")
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