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Understanding the options of atom mapping and ligandHybrid
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57
|
581
|
February 23, 2023
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Oscillational period warning during tripeptide A2I forward simulation
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14
|
541
|
January 31, 2023
|
|
Problem in using gentop
|
|
12
|
267
|
January 20, 2023
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List index out of range when running pmx gentop
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2
|
252
|
December 29, 2022
|
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Bonds that rotated more than 30 degrees:
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1
|
307
|
November 3, 2022
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IndexError: list index out of range while preparing pdb file
|
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1
|
390
|
September 15, 2022
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Ligand topolgies for pmx
|
|
5
|
462
|
September 1, 2022
|
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Pmx RBFE gives oddly large deltaG
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1
|
331
|
August 14, 2022
|
|
PMX engineered resiude
|
|
4
|
260
|
July 18, 2022
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Pmx ABFE ligand only simulation set-up
|
|
3
|
409
|
July 18, 2022
|
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Using pmx genlib and hybrid topologies
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3
|
461
|
July 11, 2022
|
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PMX generating protein ligand simulation system with Charmm/cgenff forcefields
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1
|
429
|
June 14, 2022
|
|
Free energy calculations error
|
|
1
|
1412
|
June 14, 2022
|
|
Free Energy Calculation: State B has non-zero total charge: -1.000000
|
|
1
|
354
|
June 14, 2022
|
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Free energy calculation with double system/single box simulation
|
|
12
|
477
|
March 30, 2022
|
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Error with Zn atom
|
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3
|
381
|
March 29, 2022
|
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Problem with SS bridges - Bug?
|
|
3
|
305
|
March 24, 2022
|
|
Peptide Nucleic Acid Functionality
|
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2
|
400
|
January 2, 2022
|
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Pmx - problems reproducing benchmarking from de Groot 2020
|
|
2
|
600
|
October 17, 2021
|
|
Itp ligand file generation
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|
3
|
928
|
October 14, 2021
|
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A non-finite potential energy in non-equilibrium transition with pmx
|
|
2
|
436
|
October 1, 2021
|
|
Alchemical free energy calculations
|
|
1
|
427
|
October 1, 2021
|
|
LINCS error during Alchemical free energy calculation
|
|
1
|
503
|
September 30, 2021
|
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Energy minimization of hybrid ligand
|
|
2
|
533
|
November 13, 2020
|
|
Relative constraint deviation after LINCS
|
|
6
|
1998
|
October 9, 2020
|
|
Dual Topology Generator for Alchemical Pathways
|
|
1
|
790
|
October 9, 2020
|
|
Installed - can't import _pmx as _p
|
|
3
|
966
|
July 4, 2020
|
|
Follow-Up from Webinar: Mutation free energy calculations with pmx
|
|
0
|
1486
|
June 10, 2016
|