Amber Archive Aug 2016: by date

Sunday, 31 July 2016
- [AMBER] EEL energy of QM/MM-GBSA 张姝姝
- Re: [AMBER] EEL become ****** in minimization Suguru ASAI
- Re: [AMBER] EEL become ****** in minimization David Cerutti
Monday, 1 August 2016
- Re: [AMBER] Sander bomb: how to create a larger box Ruth Helena Tichauer
- Re: [AMBER] Sander bomb: how to create a larger box Bill Ross
- Re: [AMBER] Sander bomb: how to create a larger box Ruth Helena Tichauer
- Re: [AMBER] Sander bomb: how to create a larger box Bill Ross
- Re: [AMBER] Sander bomb: how to create a larger box Ruth Helena Tichauer
- [AMBER] Use two different force fields in Amber Xiaoliu Zhang
- [AMBER] subject: parametrization of Force field DOCENTE ANTISTIO ANIBAL ALVIS AMADOR
- [AMBER] EVB calculations of proton transfer David A Case
- Re: [AMBER] Sander bomb: how to create a larger box David A Case
- Re: [AMBER] EEL energy of QM/MM-GBSA David A Case
- Re: [AMBER] EEL become ****** in minimization David A Case
- [AMBER] tinker_to_amber error Xiaoliu Zhang
- [AMBER] default value (inp= 0,1,2)? MMPBSA Thakur, Abhishek
- Re: [AMBER] hydrogen bond occupancy plot cpptraj Daniel Roe
- Re: [AMBER] Calculating Salt bridge interactions- Protein and RNA Daniel Roe
- Re: [AMBER] Difference of two trajectories Daniel Roe
- Re: [AMBER] default value (inp= 0,1,2)? MMPBSA Ray Luo
- Re: [AMBER] tinker_to_amber error Ray Luo
- Re: [AMBER] default value (inp= 0,1,2)? MMPBSA Thakur, Abhishek
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Daniel Roe
- Re: [AMBER] default value (inp= 0,1,2)? MMPBSA Ray Luo
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice
- Re: [AMBER] EVB calculations of proton transfer kenfack cyril
- [AMBER] which forcefield it is? Albert
Tuesday, 2 August 2016
- Re: [AMBER] InVacuoWithDielc JAIME RUBIO MARTINEZ
- [AMBER] HBond command Sidhu, Khushwant (Dr.)
- [AMBER] interaction entropy instead of normal mode analysis diaby
- Re: [AMBER] Energy overflow in MD with distance restraint under PBC (aMD problem?) Stephan Schott
- Re: [AMBER] Sander bomb: how to create a larger box Ruth Helena Tichauer
- Re: [AMBER] Use two different force fields in Amber David A Case
- Re: [AMBER] subject: parametrization of Force field David A Case
- Re: [AMBER] EVB calculations of proton transfer David A Case
- Re: [AMBER] Energy overflow in MD with distance restraint under PBC (aMD problem?) Daniel Roe
- Re: [AMBER] HBond command Daniel Roe
- Re: [AMBER] which forcefield it is? Amy Rice
- Re: [AMBER] which forcefield it is? Ross Walker
- [AMBER] correlated dihedral force constant Chi Jin
- [AMBER] EM in vacuum Dmitry Suplatov
- [AMBER] running RISM/MD on multi processors Jingyi Yan
- Re: [AMBER] running RISM/MD on multi processors Tyler Luchko (Lists)
- [AMBER] the phosphoric acid group is deformed 乔艳
- [AMBER] the end phosphoric acid group is deformed during simulation rain
- [AMBER] parmchk vs parmchk2 Andrew.Warden.csiro.au
Wednesday, 3 August 2016
- [AMBER] Amber´14 Solvent box simulation, something went wrong!! Stregone
- Re: [AMBER] tinker_to_amber error Xiaoliu Zhang
- [AMBER] Cyana3.97 to Amber15 pdb conversion Erik Davis
- [AMBER] gbsa parameter Thomas Evangelidis
- Re: [AMBER] gbsa parameter Hai Nguyen
- [AMBER] save Hessian nmode mmpbsa Bruno Falcone
- Re: [AMBER] gbsa parameter Daniel Roe
- Re: [AMBER] Cyana3.97 to Amber15 pdb conversion Daniel Roe
- Re: [AMBER] Amber´14 Solvent box simulation, something went wrong!! Daniel Roe
- [AMBER] Generate Polymer parameters konda003 .
- [AMBER] 180 degrees of angle in AMBER 10 Pengzhi Zhang
- [AMBER] Getting free energy (difference) from GPU simulations yunshi11 .
- Re: [AMBER] EM in vacuum David A Case
- Re: [AMBER] parmchk vs parmchk2 David A Case
- Re: [AMBER] Cyana3.97 to Amber15 pdb conversion David A Case
- Re: [AMBER] Generate Polymer parameters David A Case
- [AMBER] error in runing mdout_analyzer.py nida baig
- Re: [AMBER] error in runing mdout_analyzer.py Daniel Roe
- Re: [AMBER] error in runing mdout_analyzer.py nida baig
- [AMBER] error running production with restraint. Saman Yousuf ali
- [AMBER] solvate hexagonal box Neha Gandhi
Thursday, 4 August 2016
- Re: [AMBER] Amber´14 Solvent box simulation, something went wrong!! Stregone
- Re: [AMBER] Amber´14 Solvent box simulation, something went wrong!! Daniel Roe
- Re: [AMBER] error running production with restraint. Daniel Roe
- Re: [AMBER] error in runing mdout_analyzer.py Daniel Roe
- [AMBER] Is there a way to disable electrostatic solute-solvent interactions in PMEMD? Plotnikov, Nikolay
- Re: [AMBER] save Hessian nmode mmpbsa Bruno Falcone
- Re: [AMBER] save Hessian nmode mmpbsa Jason Swails
- [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht
- Re: [AMBER] Is there a way to disable electrostatic solute-solvent interactions in PMEMD? Jason Swails
- Re: [AMBER] interaction entropy instead of normal mode analysis Jason Swails
- Re: [AMBER] Getting free energy (difference) from GPU simulations Jason Swails
- Re: [AMBER] error running production with restraint. zoran matovic
- Re: [AMBER] error running production with restraint. zoran matovic
- Re: [AMBER] Question about usage of external QM in QM/MM Dr. Andreas W. Goetz
- Re: [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht
- Re: [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht
- Re: [AMBER] 180 degrees of angle in AMBER 10 Jason Swails
- Re: [AMBER] Question about usage of external QM in QM/MM David A Case
- [AMBER] unreadable crd files macc_200
- Re: [AMBER] unreadable crd files Adrian Roitberg
- Re: [AMBER] parmchk vs parmchk2 Andrew.Warden.csiro.au
- Re: [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht
- [AMBER] MMPBSA.py TrajError: Could not find number of frames in .mdcrd maryam azimzadehirani
- Re: [AMBER] unreadable crd files Hai Nguyen
- [AMBER] amber16/test/qmmm_DFTB Markus Kaukonen
- Re: [AMBER] Question about usage of external QM in QM/MM Dr. Andreas W. Goetz
- Re: [AMBER] amber16/test/qmmm_DFTB Dr. Andreas W. Goetz
Friday, 5 August 2016
- Re: [AMBER] error running production with restraint. zoran matovic
- Re: [AMBER] error running production with restraint. Saman Yousuf ali
- Re: [AMBER] MMPBSA.py TrajError: Could not find number of frames in .mdcrd David A Case
- Re: [AMBER] error running production with restraint. David A Case
- [AMBER] QMMM MD, Simulation does not start Stregone
- Re: [AMBER] Question about usage of external QM in QM/MM David A Case
- [AMBER] Cpptraj-PCA Warning Ilkow, Veronica
- [AMBER] Amber14 FEW for 3 trajectory free energy JoAnne Babula
- Re: [AMBER] Amber14 FEW for 3 trajectory free energy Amy Rice
- Re: [AMBER] Use two different force fields in Amber Xiaoliu Zhang
- [AMBER] Implicit solvent in pmemd.cuda Chitrak Gupta
- Re: [AMBER] Implicit solvent in pmemd.cuda Hai Nguyen
- Re: [AMBER] Implicit solvent in pmemd.cuda Carlos Simmerling
- Re: [AMBER] Implicit solvent in pmemd.cuda Ross Walker
- Re: [AMBER] Cyana3.97 to Amber15 pdb conversion Erik Davis
- Re: [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht
- [AMBER] Error with nmode calculations Praneeth Bommisetti
- Re: [AMBER] Error with nmode calculations Jason Swails
- [AMBER] restraining mean square displacements Irem Altan
- Re: [AMBER] restraining mean square displacements Adrian Roitberg
- Re: [AMBER] Question about usage of external QM in QM/MM Dr. Andreas W. Goetz
- Re: [AMBER] QMMM MD, Simulation does not start Dr. Andreas W. Goetz
- [AMBER] box of polar molecules using amoeba force field Xiaoliu Zhang
- Re: [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht
Saturday, 6 August 2016
- Re: [AMBER] error running production with restraint. Saman Yousuf ali
- Re: [AMBER] Question about usage of external QM in QM/MM Dr. Andreas W. Goetz
- [AMBER] Extend of manual modulation-Connecting two molecules methodology Kostas Bourandas
- [AMBER] How to fix the wall of the water box in amber Ming Tang
- Re: [AMBER] How to fix the wall of the water box in amber Bill Ross
- Re: [AMBER] Extend of manual modulation-Connecting two molecules methodology David A Case
- Re: [AMBER] How to fix the wall of the water box in amber Ming Tang
Sunday, 7 August 2016
- Re: [AMBER] How to fix the wall of the water box in amber Bill Ross
- Re: [AMBER] QMMM MD, Simulation does not start Stregone
- [AMBER] copy charges using Python API Thomas Evangelidis
- Re: [AMBER] copy charges using Python API Jason Swails
- Re: [AMBER] copy charges using Python API Thomas Evangelidis
- Re: [AMBER] copy charges using Python API David A Case
- Re: [AMBER] QMMM MD, Simulation does not start Daniel Roe
- Re: [AMBER] SMD simulation bharat gupta
Monday, 8 August 2016
- Re: [AMBER] MMPBSA.py TrajError: Could not find number of frames in .mdcrd maryam azimzadehirani
- Re: [AMBER] QMMM MD, Simulation does not start Stregone
- Re: [AMBER] copy charges using Python API Thomas Evangelidis
- Re: [AMBER] copy charges using Python API David A Case
- [AMBER] intel MPI failed Albert
- Re: [AMBER] intel MPI failed Daniel Roe
- Re: [AMBER] intel MPI failed Albert
- Re: [AMBER] intel MPI failed Daniel Roe
- Re: [AMBER] intel MPI failed Albert
- [AMBER] reweighting scheme Thakur, Abhishek
- Re: [AMBER] copy charges using Python API Hai Nguyen
- [AMBER] phi-psi distribution Thakur, Abhishek
- [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water Corum, Katharine W
- Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water Ayesha Fatima
- Re: [AMBER] Extend of manual modulation-Connecting two molecules methodology Kostas Bourandas
- Re: [AMBER] intel MPI failed Albert
Tuesday, 9 August 2016
- [AMBER] query regarding restraint on specific residues. Saman Yousuf ali
- [AMBER] {AMBER} installation on mac osx 10.11.6 hanging when configuring NetCDF mirko hennig
- Re: [AMBER] copy charges using Python API William Lees
- [AMBER] Off , mol2 and frcmod files Christopher Jesudason
- Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water David A Case
- Re: [AMBER] intel MPI failed David A Case
- Re: [AMBER] {AMBER} installation on mac osx 10.11.6 hanging when configuring NetCDF David A Case
- Re: [AMBER] query regarding restraint on specific residues. David A Case
- Re: [AMBER] intel MPI failed Albert
- Re: [AMBER] Off , mol2 and frcmod files David A Case
- Re: [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht
- Re: [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht
- Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water Corum, Katharine W
- Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water Marc van der Kamp
- Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water Corum, Katharine W
- [AMBER] for what kind of post simulation analysis I need to do reweighing? Thakur, Abhishek
- Re: [AMBER] for what kind of post simulation analysis I need to do reweighing? Adrian Roitberg
- Re: [AMBER] query regarding restraint on specific residues. Saman Yousuf ali
- Re: [AMBER] for what kind of post simulation analysis I need to do reweighing? Thakur, Abhishek
- Re: [AMBER] {AMBER} installation on mac osx 10.11.6 hanging when configuring NetCDF mirko hennig
- [AMBER] simultaneous use of ibelly=1 and ntr=1 Saman Yousuf ali
- Re: [AMBER] for what kind of post simulation analysis I need to do reweighing? Christina Bergonzo
- Re: [AMBER] Amber14 FEW for 3 trajectory free energy JoAnne Babula
- Re: [AMBER] Question about usage of external QM in QM/MM David A Case
- Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water David A Case
- Re: [AMBER] simultaneous use of ibelly=1 and ntr=1 David A Case
- Re: [AMBER] simultaneous use of ibelly=1 and ntr=1 Saman Yousuf ali
- Re: [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht
- [AMBER] Converting rst to pdb Corum, Katharine W
- Re: [AMBER] Converting rst to pdb Hai Nguyen
- Re: [AMBER] Converting rst to pdb Daniel Roe
- Re: [AMBER] Question about usage of external QM in QM/MM Dr. Andreas W. Goetz
- Re: [AMBER] Converting rst to pdb Corum, Katharine W
Wednesday, 10 August 2016
- [AMBER] Amber 14.13 pmemd.cuda: Error: invalid configuration argument launching kernel kPMEReduceChargeGridBuffer William Lees
- [AMBER] does AMBER already have Pt parameters for modeling cisplatin like compounds? Vaibhav Dixit
- Re: [AMBER] does AMBER already have Pt parameters for modeling cisplatin like compounds? Pengfei Li
- [AMBER] 3 trajectory MMPBSA free energy calculation JoAnne Babula
- Re: [AMBER] 3 trajectory MMPBSA free energy calculation Amy Rice
- [AMBER] Regarding antechamber command Error Vishal Nemaysh
- Re: [AMBER] 3 trajectory MMPBSA free energy calculation JoAnne Babula
- [AMBER] paper describing the ff15ipq protein force field is now available David A Case
- Re: [AMBER] paper describing the ff15ipq protein force field is now available David Cerutti
- [AMBER] antechamber cannot match patching atoms of amino acid Chitrak Gupta
- Re: [AMBER] Amber 14.13 pmemd.cuda: Error: invalid configuration argument launching kernel kPMEReduceChargeGridBuffer Ross Walker
Thursday, 11 August 2016
- [AMBER] Fwd: Regarding antechamber command Error Vishal Nemaysh
- [AMBER] GPU MPI failed Albert
- Re: [AMBER] Regarding antechamber command Error David A Case
- Re: [AMBER] antechamber cannot match patching atoms of amino acid David A Case
- Re: [AMBER] GPU MPI failed David A Case
- Re: [AMBER] Regarding antechamber command Error Vishal Nemaysh
- Re: [AMBER] GPU MPI failed Albert
- [AMBER] Amber16 installation error. Abhilash J
- [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula
- [AMBER] secondary structure graph vs Time Parviz Seifpanahi Shabane
- Re: [AMBER] secondary structure graph vs Time Adrian Roitberg
- Re: [AMBER] secondary structure graph vs Time Parviz Seifpanahi Shabane
- Re: [AMBER] secondary structure graph vs Time Adrian Roitberg
- [AMBER] Running tleap with old prmtop Taylor Quinn
- Re: [AMBER] Running tleap with old prmtop Samuel Bowerman
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Hai Nguyen
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Hai Nguyen
- Re: [AMBER] Amber16 installation error. Hai Nguyen
- Re: [AMBER] Amber16 installation error. Abhilash J
- Re: [AMBER] Amber16 installation error. Hai Nguyen
- Re: [AMBER] Amber16 installation error. Abhilash J
- Re: [AMBER] Regarding antechamber command Error David A Case
- Re: [AMBER] Amber16 installation error. Hai Nguyen
- Re: [AMBER] Amber16 installation error. Abhilash J
- Re: [AMBER] Amber16 installation error. Hai Nguyen
- Re: [AMBER] Amber16 installation error. Abhilash J
- Re: [AMBER] Amber16 installation error. Hai Nguyen
- Re: [AMBER] Amber16 installation error. Hai Nguyen
- Re: [AMBER] Amber16 installation error. Abhilash J
- Re: [AMBER] Amber16 installation error. Hai Nguyen
- Re: [AMBER] Amber16 installation error. Abhilash J
- [AMBER] GPU peer support disabled Hirdesh Kumar
- Re: [AMBER] Amber16 installation error. Abhilash J
- Re: [AMBER] GPU peer support disabled Ross Walker
- Re: [AMBER] Amber16 installation error. Hai Nguyen
- Re: [AMBER] GPU peer support disabled Hirdesh Kumar
- Re: [AMBER] Amber16 installation error. Abhilash J
- [AMBER] LINMIN FAILURE on large protein minimization with GB and explicit SUNHEE CHO
- Re: [AMBER] LINMIN FAILURE on large protein minimization with GB and explicit Ross Walker
- Re: [AMBER] Amber16 Parallel CUDA Tests Steven Ford
- Re: [AMBER] Amber16 Parallel CUDA Tests Ross Walker
- [AMBER] not sure if this is an ERROR in installation please suggest Vaibhav Dixit
- Re: [AMBER] Amber16 Parallel CUDA Tests Steven Ford
- Re: [AMBER] Amber16 Parallel CUDA Tests Ross Walker
- Re: [AMBER] not sure if this is an ERROR in installation please suggest Ross Walker
- Re: [AMBER] Amber16 Parallel CUDA Tests Steven Ford
- Re: [AMBER] Amber16 Parallel CUDA Tests Steven Ford
- Re: [AMBER] Amber16 Parallel CUDA Tests Ross Walker
- Re: [AMBER] not sure if this is an ERROR in installation please suggest Hai Nguyen
- Re: [AMBER] Regarding antechamber command Error Vishal Nemaysh
Friday, 12 August 2016
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Bilal Nizami
- Re: [AMBER] not sure if this is an ERROR in installation please suggest Vaibhav Dixit
- [AMBER] amber pdb > 100,000 atoms Neha Gandhi
- Re: [AMBER] antechamber cannot match patching atoms of amino acid FyD
- Re: [AMBER] amber pdb > 100,000 atoms Marc van der Kamp
- [AMBER] modeling flexible loops in protein-DNA complexes Vlad Cojocaru
- Re: [AMBER] secondary structure graph vs Time Prajwal Nandekar
- Re: [AMBER] LINMIN FAILURE on large protein minimization with GB and explicit David A Case
- Re: [AMBER] Regarding antechamber command Error David A Case
- Re: [AMBER] amber pdb > 100,000 atoms David A Case
- Re: [AMBER] Amber 14.13 pmemd.cuda: Error: invalid configuration argument launching kernel kPMEReduceChargeGridBuffer William Lees
- [AMBER] Optimal force constant for AMBER Stregone
- [AMBER] job suspended Albert
- Re: [AMBER] not sure if this is an ERROR in installation please suggest Hai Nguyen
- Re: [AMBER] Optimal force constant for AMBER David A Case
- Re: [AMBER] job suspended David A Case
- Re: [AMBER] job suspended Albert
- Re: [AMBER] job suspended Nhai
- [AMBER] MASK with distance in AMBER. Parviz Seifpanahi Shabane
- Re: [AMBER] Amber16 Parallel CUDA Tests Steven Ford
- [AMBER] umbrella sampling restraining both angle and distance Thakur, Abhishek
- [AMBER] cpptraj issues Thomas Pochapsky
- [AMBER] Two ion problem with mcpb.py Abhilash J
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Amy Rice
- Re: [AMBER] MASK with distance in AMBER. Daniel Roe
- Re: [AMBER] cpptraj issues Daniel Roe
- [AMBER] Amber B5 tutorial Chitrak Gupta
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Hai Nguyen
- Re: [AMBER] Amber B5 tutorial David A Case
- Re: [AMBER] Two ion problem with mcpb.py sunita guptacDgug
- [AMBER] Accelerated MD -- cudaMemcpy error Dmitry Suplatov
- Re: [AMBER] umbrella sampling restraining both angle and distance Carlos Simmerling
- Re: [AMBER] umbrella sampling restraining both angle and distance Thakur, Abhishek
- [AMBER] Question of Parameter Defaults Robert Molt
Saturday, 13 August 2016
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Bilal Nizami
- Re: [AMBER] Question of Parameter Defaults Carlos Simmerling
- Re: [AMBER] Question of Parameter Defaults David A Case
- [AMBER] job failed Albert
Sunday, 14 August 2016
- [AMBER] error in sander and sander.mpi running leila karami
- [AMBER] error in sander and sander.mpi running leila karami
- Re: [AMBER] job failed David A Case
- Re: [AMBER] umbrella sampling restraining both angle and distance Carlos Simmerling
- [AMBER] solid surface simulation in amber Neha Gandhi
Monday, 15 August 2016
- Re: [AMBER] parmchk vs parmchk2 Hannes Loeffler
- Re: [AMBER] Accelerated MD -- cudaMemcpy error DmitryASuplatov
- Re: [AMBER] solid surface simulation in amber David A Case
- [AMBER] Fwd: cpptraj issues Thomas Pochapsky
- [AMBER] parmchk2 issue Hannes Loeffler
- [AMBER] QM/MM stops at step 2114 Corum, Katharine W
- Re: [AMBER] parmchk2 issue David A Case
- Re: [AMBER] QM/MM stops at step 2114 David A Case
- [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan mirko hennig
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan Hai Nguyen
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan David A Case
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan mirko hennig
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan Hai Nguyen
- Re: [AMBER] Fwd: cpptraj issues Daniel Roe
- Re: [AMBER] Question of Parameter Defaults Robert Molt
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan mirko hennig
- Re: [AMBER] Accelerated MD -- cudaMemcpy error Daniel Roe
- Re: [AMBER] secondary structure graph vs Time Parviz Seifpanahi Shabane
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan David A Case
- [AMBER] CHARM force field Chi Jin
- Re: [AMBER] secondary structure graph vs Time Daniel Roe
- Re: [AMBER] CHARM force field Jason Swails
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan Jason Swails
- [AMBER] bellymask option. Saman Yousuf ali
- Re: [AMBER] solid surface simulation in amber Neha Gandhi
Tuesday, 16 August 2016
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan mirko hennig
- Re: [AMBER] solid surface simulation in amber Bill Ross
- Re: [AMBER] solid surface simulation in amber Neha Gandhi
- Re: [AMBER] solid surface simulation in amber Bill Ross
- Re: [AMBER] parmchk2 issue Hannes Loeffler
- [AMBER] lipid simulation with Lipid14 FF failed Albert
- Re: [AMBER] Accelerated MD -- cudaMemcpy error DmitryASuplatov
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan David A Case
- Re: [AMBER] bellymask option. David A Case
- Re: [AMBER] solid surface simulation in amber David A Case
- Re: [AMBER] parmchk2 issue David A Case
- Re: [AMBER] lipid simulation with Lipid14 FF failed David A Case
- Re: [AMBER] lipid simulation with Lipid14 FF failed Albert
- Re: [AMBER] solid surface simulation in amber Neha Gandhi
- Re: [AMBER] QM/MM stops at step 2114 Corum, Katharine W
- Re: [AMBER] parmchk2 issue Hannes Loeffler
- Re: [AMBER] lipid simulation with Lipid14 FF failed Ross Walker
- [AMBER] Fwd: cpptraj issues Thomas Pochapsky
- Re: [AMBER] Two ion problem with mcpb.py Pengfei Li
- Re: [AMBER] error in sander and sander.mpi running Daniel Roe
- Re: [AMBER] bellymask option. Saman Yousuf ali
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan mirko hennig
- Re: [AMBER] Fwd: cpptraj issues Daniel Roe
- Re: [AMBER] solid surface simulation in amber Daniel Roe
- Re: [AMBER] Accelerated MD -- cudaMemcpy error Daniel Roe
- Re: [AMBER] Fwd: cpptraj issues Thomas Pochapsky
- Re: [AMBER] secondary structure graph vs Time Parviz Seifpanahi Shabane
- [AMBER] Water flexibility in QM/MM simulation Ruth Helena Tichauer
- [AMBER] Restarting a crushed run DmitryASuplatov
- [AMBER] Regarding the free energy calculation Sivanandam M
- Re: [AMBER] MASK with distance in AMBER. Parviz Seifpanahi Shabane
- Re: [AMBER] Restarting a crushed run Bill Ross
- Re: [AMBER] Restarting a crushed run Bill Ross
- Re: [AMBER] Restarting a crushed run Dmitry Suplatov
- Re: [AMBER] Restarting a crushed run Dmitry Suplatov
- [AMBER] Combining single structure NMR pdb files into an ensemble. Erik Davis
- Re: [AMBER] Combining single structure NMR pdb files into an ensemble. Hai Nguyen
- Re: [AMBER] parmchk2 issue David A Case
- Re: [AMBER] Restarting a crushed run Bill Ross
- Re: [AMBER] Restarting a crushed run Ross Walker
Wednesday, 17 August 2016
- [AMBER] about lipids retrain Albert
- Re: [AMBER] about lipids retrain David A Case
- Re: [AMBER] about lipids retrain Albert
- [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Cecilia Lindgren
- Re: [AMBER] Combining single structure NMR pdb files into an ensemble. Erik Davis
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server David A Case
- Re: [AMBER] MASK with distance in AMBER. Daniel Roe
- [AMBER] Is there any CG martini parameter for K+? li he
- [AMBER] Problem when visualizing bonds in VMD Xiaoliu Zhang
- Re: [AMBER] Problem when visualizing bonds in VMD Jason Swails
- Re: [AMBER] Is there any CG martini parameter for K+? Pengfei Li
- [AMBER] QM region has an odd number of electrons Corum, Katharine W
- Re: [AMBER] QM region has an odd number of electrons Dr. Andreas W. Goetz
- [AMBER] RMSd Wong Li Zhe
- Re: [AMBER] RMSd Hai Nguyen
- Re: [AMBER] RMSd Wong Li Zhe
- Re: [AMBER] RMSd Wong Li Zhe
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Cecilia Lindgren
- Re: [AMBER] RMSd Bill Ross
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Bill Ross
Thursday, 18 August 2016
- Re: [AMBER] solid surface simulation in amber Neha Gandhi
- Re: [AMBER] solid surface simulation in amber Bill Ross
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Cecilia Lindgren
- Re: [AMBER] solid surface simulation in amber Neha Gandhi
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Bill Ross
- [AMBER] LEaP and PARMSETs Aronica, Pietro
- Re: [AMBER] solid surface simulation in amber Bill Ross
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Cecilia Lindgren
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Bill Ross
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Hannes Loeffler
- [AMBER] a bug in leaprc.gaff2 file Ye Mei
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Bill Ross
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Cecilia Lindgren
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan Jason Swails
- Re: [AMBER] solid surface simulation in amber David A Case
- Re: [AMBER] a bug in leaprc.gaff2 file David A Case
- Re: [AMBER] a bug in leaprc.gaff2 file David A Case
- [AMBER] Problem in charge generation through antechamber ATUL KUMAR
- Re: [AMBER] Two ion problem with mcpb.py Abhilash J
- Re: [AMBER] Problem in charge generation through antechamber Bruno Falcone
- Re: [AMBER] Problem in charge generation through antechamber ATUL KUMAR
- Re: [AMBER] Problem in charge generation through antechamber David A Case
- Re: [AMBER] Problem in charge generation through antechamber Bruno Falcone
- Re: [AMBER] Problem when visualizing bonds in VMD Xiaoliu Zhang
- Re: [AMBER] Problem when visualizing bonds in VMD Hai Nguyen
- Re: [AMBER] Two ion problem with mcpb.py Pengfei Li
- [AMBER] percentages of protein secondary structure. Saman Yousuf ali
- Re: [AMBER] Two ion problem with mcpb.py Abhilash J
- Re: [AMBER] percentages of protein secondary structure. Nhai
- Re: [AMBER] Problem in charge generation through antechamber ATUL KUMAR
- [AMBER] Does Scaled MD require NVT ensemble? Harshavardhan Khare
Friday, 19 August 2016
- [AMBER] Temperature Shoot-up in TMD Aravind Ravichandran
- Re: [AMBER] Temperature Shoot-up in TMD Bill Ross
- Re: [AMBER] solid surface simulation in amber Neha Gandhi
- [AMBER] What cutoff you use in Amber simulations? DmitryASuplatov
- Re: [AMBER] Temperature Shoot-up in TMD Carlos Simmerling
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan Jason Swails
- Re: [AMBER] What cutoff you use in Amber simulations? Jason Swails
- Re: [AMBER] Does Scaled MD require NVT ensemble? Ross Walker
- [AMBER] Tutorial B5 - Loading CRO from ccif file Alfredo Quevedo
- Re: [AMBER] Problem in charge generation through antechamber Bruno Falcone
- Re: [AMBER] percentages of protein secondary structure. Hai Nguyen
- Re: [AMBER] solid surface simulation in amber David A Case
- Re: [AMBER] Tutorial B5 - Loading CRO from ccif file David A Case
- Re: [AMBER] Tutorial B5 - Loading CRO from ccif file Alfredo Quevedo
- Re: [AMBER] Regarding the free energy calculation Daniel Mermelstein
- [AMBER] concerns on membrane protein restrain Albert
- Re: [AMBER] Problem when visualizing bonds in VMD Xiaoliu Zhang
- Re: [AMBER] solid surface simulation in amber Bill Ross
- Re: [AMBER] Problem when visualizing bonds in VMD Nhai
- [AMBER] WHAM analysis Thakur, Abhishek
- Re: [AMBER] solid surface simulation in amber Neha Gandhi
- Re: [AMBER] solid surface simulation in amber Bill Ross
- Re: [AMBER] Does Scaled MD require NVT ensemble? Harshavardhan Khare
Saturday, 20 August 2016
- Re: [AMBER] WHAM analysis Chi Jin
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server FyD
- Re: [AMBER] Problem in charge generation through antechamber FyD
- Re: [AMBER] WHAM analysis Amy Rice
- Re: [AMBER] WHAM analysis Chi Jin
- Re: [AMBER] WHAM analysis Adrian Roitberg
Sunday, 21 August 2016
- [AMBER] minimum restraint_wt. Saman Yousuf ali
- [AMBER] Frac in cpptraj hydrogen bond command. Saman Yousuf ali
- Re: [AMBER] Frac in cpptraj hydrogen bond command. Daniel Roe
Monday, 22 August 2016
- Re: [AMBER] solid surface simulation in amber Neha Gandhi
- Re: [AMBER] solid surface simulation in amber Bill Ross
- Re: [AMBER] solid surface simulation in amber Neha Gandhi
- [AMBER] Adaptively Biased MD Simulations of type "distance" using "FLOODING" Emmanuel
- Re: [AMBER] Adaptively Biased MD Simulations of type "distance" using "FLOODING" Bill Ross
- Re: [AMBER] Adaptively Biased MD Simulations of type "distance" using "FLOODING" Bill Ross
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula
- Re: [AMBER] Adaptively Biased MD Simulations of type "distance" using "FLOODING" Feng Pan
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Nhai
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Nhai
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Hai Nguyen
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Hai Nguyen
- [AMBER] Sigma and epsilon vdw parameters Neha Gandhi
- Re: [AMBER] Sigma and epsilon vdw parameters Bill Ross
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula
- [AMBER] Output Files Wong Li Zhe
- Re: [AMBER] Output Files Hai Nguyen
- [AMBER] Simulation Time Wong Li Zhe
Tuesday, 23 August 2016
- [AMBER] Alanine scan of nonnatural amino acid Aronica, Pietro
- Re: [AMBER] minimum restraint_wt. David A Case
- [AMBER] Copper +1 and membrane with LJ 12-6-4 potential Stephan Schott
- Re: [AMBER] Alanine scan of nonnatural amino acid Jason Swails
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Jason Swails
- [AMBER] Problem with atommap function in cpptraj (v16) Samuel Bowerman
- [AMBER] Generating parameter and topology files for a protein with multiple Zinc ions Aditya Padhi
- [AMBER] Checking modeling after MCPB and unable to fix atom order using cpptraj Andrew Schaub
- Re: [AMBER] Checking modeling after MCPB and unable to fix atom order using cpptraj Hai Nguyen
- Re: [AMBER] Checking modeling after MCPB and unable to fix atom order using cpptraj Andrew Schaub
- [AMBER] Generating topology and parameter file for a peptide pratibha sharma
- Re: [AMBER] Generating topology and parameter file for a peptide Hai Nguyen
Wednesday, 24 August 2016
- Re: [AMBER] Generating topology and parameter file for a peptide Bill Ross
- [AMBER] 22.1.6.1. Free Energy using linear scaling 22.1.6.2.Absolute free energy using soft core, Markus Kaukonen
- [AMBER] cpptraj on pH-REMD Elisa Pieri
- Re: [AMBER] Simulation Time Dd H
- Re: [AMBER] 22.1.6.1. Free Energy using linear scaling 22.1.6.2.Absolute free energy using soft core, Hannes Loeffler
- [AMBER] Regarding hbond bridgeout Indrajit Deb
- [AMBER] Issues compiling Amber with CUDA support Sivy, Shawn
- Re: [AMBER] cpptraj on pH-REMD Jason Swails
- Re: [AMBER] Generating parameter and topology files for a protein with multiple Zinc ions Bill Ross
Thursday, 25 August 2016
- [AMBER] SEP parameter with ff15ipq vadiraj kurdekar
- [AMBER] Problem with rst7 Elisa Pieri
- Re: [AMBER] Problem with rst7 Bill Ross
- [AMBER] Fw: Problems to calculate frequencies Stregone
- Re: [AMBER] Problem with rst7 Carlos Simmerling
- [AMBER] output of MMPBSA.py Markus Kaukonen
- Re: [AMBER] output of MMPBSA.py Bilal Nizami
- Re: [AMBER] Problem with rst7 Elisa Pieri
- Re: [AMBER] Problem with rst7 Carlos Simmerling
- Re: [AMBER] SEP parameter with ff15ipq David A Case
- Re: [AMBER] Fw: Problems to calculate frequencies David A Case
- Re: [AMBER] SEP parameter with ff15ipq David Cerutti
- [AMBER] MMPBSA.py CalcError on ligand contribution only Leandro Bortot
- [AMBER] problem upon optimization giulia palermo
- Re: [AMBER] problem upon optimization Adrian Roitberg
- Re: [AMBER] problem upon optimization Jason Swails
- Re: [AMBER] MMPBSA.py CalcError on ligand contribution only Jason Swails
- Re: [AMBER] Issues compiling Amber with CUDA support Ross Walker
- [AMBER] Checking AmberTools16 installation Bence Hégely
- Re: [AMBER] Checking AmberTools16 installation Hai Nguyen
- Re: [AMBER] MMPBSA.py CalcError on ligand contribution only Leandro Bortot
- [AMBER] repair mdcrd? Bill Ross
- Re: [AMBER] repair mdcrd? Hai Nguyen
- Re: [AMBER] problem upon optimization giulia palermo
- Re: [AMBER] repair mdcrd? Bill Ross
- Re: [AMBER] repair mdcrd? Daniel Roe
- Re: [AMBER] MMPBSA.py CalcError on ligand contribution only Jason Swails
- Re: [AMBER] SEP parameter with ff15ipq vadiraj kurdekar
Friday, 26 August 2016
- [AMBER] begin time read from input coords Hannes Loeffler
- Re: [AMBER] begin time read from input coords Daniel Roe
- Re: [AMBER] begin time read from input coords Hannes Loeffler
- [AMBER] Multihist in watershell command Damiano Spadoni
- Re: [AMBER] begin time read from input coords David A Case
- Re: [AMBER] SEP parameter with ff15ipq Carlos Simmerling
- Re: [AMBER] Checking AmberTools16 installation Bence Hégely
- Re: [AMBER] begin time read from input coords Hannes Loeffler
- Re: [AMBER] Multihist in watershell command Hai Nguyen
- Re: [AMBER] Multihist in watershell command Daniel Roe
- Re: [AMBER] Regarding hbond bridgeout Daniel Roe
- Re: [AMBER] Problem with atommap function in cpptraj (v16) Daniel Roe
Saturday, 27 August 2016
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan mirko hennig
- Re: [AMBER] Issues compiling Amber with CUDA support Baker, Joseph
- Re: [AMBER] Copper +1 and membrane with LJ 12-6-4 potential Pengfei Li
- Re: [AMBER] Generating parameter and topology files for a protein with multiple Zinc ions Pengfei Li
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan Nhai
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan mirko hennig
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan Bill Ross
- Re: [AMBER] Issues compiling Amber with CUDA support Ross Walker
- [AMBER] (no subject) Amrullah13
- Re: [AMBER] (no subject) Hai Nguyen
- Re: [AMBER] Issues compiling Amber with CUDA support Baker, Joseph
Monday, 29 August 2016
- [AMBER] autoimage bug? Filip Persson
- [AMBER] autocorr of hydrogen bonds Osman, Roman
- [AMBER] errors in doing TI tutorial calculation 张姝姝
- Re: [AMBER] (no subject) Jason Swails
- Re: [AMBER] Checking AmberTools16 installation Hai Nguyen
- Re: [AMBER] errors in doing TI tutorial calculation David A Case
- Re: [AMBER] errors in doing TI tutorial calculation Hannes Loeffler
Tuesday, 30 August 2016
- [AMBER] restraint does not work in mininmization Michael Shokhen
- Re: [AMBER] restraint does not work in mininmization Hirdesh Kumar
- [AMBER] frozen geometry setting? Michael Shokhen
- Re: [AMBER] Checking AmberTools16 installation Bence Hégely
- Re: [AMBER] autocorr of hydrogen bonds Tom Kurtzman
- Re: [AMBER] Checking AmberTools16 installation Hai Nguyen
- Re: [AMBER] frozen geometry setting? David A Case
- Re: [AMBER] Checking AmberTools16 installation Hai Nguyen
- [AMBER] Parameters for modified nucleosides Tomek Wlodarski
- Re: [AMBER] frozen geometry setting? Michael Shokhen
- Re: [AMBER] frozen geometry setting? Bill Ross
- Re: [AMBER] frozen geometry setting? Michael Shokhen
- Re: [AMBER] frozen geometry setting? Adrian Roitberg
- Re: [AMBER] frozen geometry setting? Bill Ross
- Re: [AMBER] Problem with atommap function in cpptraj (v16) Samuel Bowerman
- Re: [AMBER] autocorr of hydrogen bonds Osman, Roman
- [AMBER] lowering the temperature Thomas Evangelidis
- Re: [AMBER] lowering the temperature Carlos Simmerling
Wednesday, 31 August 2016
- [AMBER] change the atom charge in a restart simulations windy
- Re: [AMBER] change the atom charge in a restart simulations Bill Ross
- Re: [AMBER] lowering the temperature Thomas Evangelidis
- Re: [AMBER] lowering the temperature Carlos Simmerling
- Re: [AMBER] change the atom charge in a restart simulations David A Case
- Re: [AMBER] Problem with atommap function in cpptraj (v16) Daniel Roe
- Re: [AMBER] autoimage bug? Daniel Roe
- Re: [AMBER] frozen geometry setting? Michael Shokhen
- [AMBER] changing atom type Jacopo Sgrignani
- Re: [AMBER] changing atom type Hai Nguyen
- Re: [AMBER] Multihist in watershell command Damiano Spadoni
- [AMBER] QM/MM energy units? Corum, Katharine W
- Re: [AMBER] QM/MM energy units? Jacopo Sgrignani
- Re: [AMBER] QM/MM energy units? Adrian Roitberg
- Re: [AMBER] QM/MM energy units? Corum, Katharine W
- Re: [AMBER] changing atom type Jason Swails
- [AMBER] File redirection commands with targeted MD Sonia Ziada
- [AMBER] Amber Force Fields amir sadeghi
- Re: [AMBER] Amber Force Fields Hai Nguyen
- [AMBER] Regarding the use of sed command to replace water Budhathoki, Dipesh
- Re: [AMBER] Regarding the use of sed command to replace water Corum, Katharine W
- Re: [AMBER] Regarding the use of sed command to replace water Adrian Roitberg
- Re: [AMBER] Regarding the use of sed command to replace water David A Case
- Re: [AMBER] changing atom type Dr. Andreas W. Goetz
- Re: [AMBER] Regarding the use of sed command to replace water Budhathoki, Dipesh
- Re: [AMBER] Amber Force Fields Carlos Simmerling

Last message date: Wed Aug 31 2016 - 18:00:02 PDT
Archived on: Wed Dec 25 2024 - 05:55:24 PST

Amber Archive Aug 2016 by date