Amber Archive Nov 2016: by date

Tuesday, 1 November 2016
- [AMBER] mmpbsa error 东不拉
- Re: [AMBER] [mdout_analyzer.py] Problem with OS X El Capitan Eiros Zamora, Juan
- Re: [AMBER] [mdout_analyzer.py] Problem with OS X El Capitan Eiros Zamora, Juan
- Re: [AMBER] [mdout_analyzer.py] Problem with OS X El Capitan Jason Swails
- [AMBER] MCPB problems Fabrício Bracht
- [AMBER] problem with MMPBSApy in Amber 16 Marek Maly
- Re: [AMBER] problem with MMPBSApy in Amber 16 Ray Luo
- Re: [AMBER] MCPB problems Pengfei Li
- Re: [AMBER] MCPB problems Fabrício Bracht
- Re: [AMBER] MCPB problems Fabrício Bracht
- [AMBER] The ultimate temperature is 11K instead of 100K in heating simulation Nikolay N. Kuzmich
- Re: [AMBER] mmpbsa error Ray Luo
- Re: [AMBER] problem with MMPBSApy in Amber 16 Marek Maly
- Re: [AMBER] The ultimate temperature is 11K instead of 100K in heating simulation Ross Walker
- Re: [AMBER] problem with MMPBSApy in Amber 16 Ray Luo
- Re: [AMBER] problem with MMPBSApy in Amber 16 Marek Maly
- Re: [AMBER] problem with MMPBSApy in Amber 16 Ray Luo
- Re: [AMBER] problem with MMPBSApy in Amber 16 Ray Luo
- Re: [AMBER] problem with MMPBSApy in Amber 16 Marek Maly
Wednesday, 2 November 2016
- [AMBER] Gromber failed. Dd H
- [AMBER] Simulation of protein in lipid blayer using GB solvation model Nikolay N. Kuzmich
- Re: [AMBER] Simulation of protein in lipid blayer using GB solvation model Carlos Simmerling
- Re: [AMBER] Gromber failed. Jason Swails
- [AMBER] Problem installing Amber 16 on mac OS El Capitan Ruth Helena Tichauer
- [AMBER] MMGBSA: estimating "effective energy" convergence George Tzotzos
- Re: [AMBER] MMGBSA: estimating "effective energy" convergence Casalini Tommaso
- Re: [AMBER] Can we combine amber and gaff atom types? Aditya G Rao
- Re: [AMBER] Problem installing Amber 16 on mac OS El Capitan Hai Nguyen
- Re: [AMBER] Can we combine amber and gaff atom types? Carlos Simmerling
- [AMBER] micro iterations in QM/MM optimization. Yigal Lahav
- Re: [AMBER] MMGBSA: estimating "effective energy" convergence George Tzotzos
- Re: [AMBER] Problem installing Amber 16 on mac OS El Capitan Ruth Helena Tichauer
- [AMBER] Problem with bonds in NAB Vladislav Sláma
- Re: [AMBER] micro iterations in QM/MM optimization. Dr. Andreas W. Goetz
- [AMBER] Generating parameters of HEME Ramin Ekhteiari
- Re: [AMBER] Generating parameters of HEME Hai Nguyen
- [AMBER] How to visualize modes obtained from NMA The Cromicus Productions
- Re: [AMBER] Generating parameters of HEME David A Case
- [AMBER] Software announcement: Release of PUPIL 3.1 Joan Torras
- Re: [AMBER] Can we combine amber and gaff atom types? David Cerutti
- Re: [AMBER] Generating parameters of HEME Elvis Martis
- [AMBER] Error in the production of heat.rst file Stacyann Nelson
- Re: [AMBER] Gromber failed. Dd H
- Re: [AMBER] Gromber failed. Hai Nguyen
- Re: [AMBER] Gromber failed. Dd H
- Re: [AMBER] Gromber failed. Nhai
- Re: [AMBER] Gromber failed. Dd H
- Re: [AMBER] MCPB problems Pengfei Li
- Re: [AMBER] Error in the production of heat.rst file Elvis Martis
- Re: [AMBER] Error in the production of heat.rst file Stacyann Nelson
- Re: [AMBER] Error in the production of heat.rst file Elvis Martis
Thursday, 3 November 2016
- Re: [AMBER] MCPB.py Mahmood Jasim
- Re: [AMBER] Gromber failed. Jason Swails
- Re: [AMBER] Problem with bonds in NAB David A Case
- Re: [AMBER] Error in the production of heat.rst file David A Case
- [AMBER] RESP routine not found Marcelo Depólo
- [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Andreas Tosstorff
- Re: [AMBER] Gromber failed. Dd H
- [AMBER] cpptraj error: 'cluster': Command not found. Ruth Helena Tichauer
- Re: [AMBER] Can we combine amber and gaff atom types? Aditya G Rao
- Re: [AMBER] RESP routine not found Hai Nguyen
- Re: [AMBER] Can we combine amber and gaff atom types? David Cerutti
- [AMBER] MD simulations, DDR4 2133MHz vs 3200MHz Nikolay N. Kuzmich
- [AMBER] Failed to install mpirun Nikolay N. Kuzmich
- Re: [AMBER] Failed to install mpirun Adrian Roitberg
- Re: [AMBER] MD simulations, DDR4 2133MHz vs 3200MHz David Cerutti
- Re: [AMBER] Failed to install mpirun Charles Lin
- Re: [AMBER] Failed to install mpirun Charles Lin
- Re: [AMBER] Error in the production of heat.rst file Stacyann Nelson
- Re: [AMBER] Error in the production of heat.rst file Hai Nguyen
- Re: [AMBER] cpptraj error: 'cluster': Command not found. Daniel Roe
- [AMBER] Potential energy fluctuation of NVT ensemble Zhe Li
- [AMBER] Quenstions about pmemd.cuda.MPI Pengfei Li
- Re: [AMBER] Quenstions about pmemd.cuda.MPI Ross Walker
- [AMBER] do_debugf changes energy Ulf Ryde
- Re: [AMBER] do_debugf changes energy David Cerutti
Friday, 4 November 2016
- [AMBER] Fw:problems for running step 2 of MCPB.py 杨满意
- Re: [AMBER] do_debugf changes energy Ulf Ryde
- [AMBER] ntt = 6 and ibelly = 1 Xiangyu Jia
- Re: [AMBER] cpptraj error: 'cluster': Command not found. Ruth Helena Tichauer
- [AMBER] virtual box in gas phase simulation Xiangyu Jia
- [AMBER] Umbrella simulation with an arbitrary bias potential diego.soler.uam.es
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered David A Case
- [AMBER] Uridine diphosphate (UDP) - tleap Anna Cebrian Prats
- [AMBER] Are Intel compilers free for academics? David A Case
- [AMBER] RNA backbone dihedral restraints question Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] RNA backbone dihedral restraints question Carlos Simmerling
- Re: [AMBER] RNA backbone dihedral restraints question Kasprzak, Wojciech (NIH/NCI) [C]
- [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? Eric Lang
- Re: [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? Carlos Simmerling
- [AMBER] can not find chamber in amber16? Neale, Christopher Andrew
- Re: [AMBER] can not find chamber in amber16? Nhai
- Re: [AMBER] Uridine diphosphate (UDP) - tleap David A Case
- Re: [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? Jason Swails
- [AMBER] Potential energy fluctuation of NVT ensemble Zhe Li
- Re: [AMBER] Potential energy fluctuation of NVT ensemble Niel Henriksen
Saturday, 5 November 2016
- [AMBER] Hello! Distance restraint problems in SANDER tanfei777.sina.cn
- Re: [AMBER] Potential energy fluctuation of NVT ensemble diego.soler.uam.es
- [AMBER] MM-PBSA calculation for HEME-contained protein Ramin Ekhteiari
- Re: [AMBER] MM-PBSA calculation for HEME-contained protein Elvis Martis
- Re: [AMBER] Potential energy fluctuation of NVT ensemble Zhe Li
- Re: [AMBER] Hello! Distance restraint problems in SANDER David A Case
Sunday, 6 November 2016
- Re: [AMBER] Quenstions about pmemd.cuda.MPI Pengfei Li
- Re: [AMBER] Ligand across membrane zoran matovic
Monday, 7 November 2016
- Re: [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? Eric Lang
- Re: [AMBER] Umbrella simulation with an arbitrary bias potential David A Case
- Re: [AMBER] Umbrella simulation with an arbitrary bias potential Vlad Cojocaru
- Re: [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? Adrian Roitberg
- Re: [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? Carlos Simmerling
- Re: [AMBER] Quenstions about pmemd.cuda.MPI Ross Walker
- [AMBER] enhanced sampling conformations by AMD Kat G
- Re: [AMBER] Umbrella simulation with an arbitrary bias potential Feng Pan
Tuesday, 8 November 2016
- [AMBER] Performance drop for large systems Andreas Tosstorff
- [AMBER] Coordinates for PEG4K, Folic acid and chitin Abdul Ajees
- Re: [AMBER] RNA backbone dihedral restraints question Carlos Simmerling
- [AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped) Michael Shokhen
- Re: [AMBER] Performance drop for large systems Ross Walker
- Re: [AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped) Samuel Bowerman
- Re: [AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped) Daniel Roe
- Re: [AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped) Michael Shokhen
- Re: [AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped) Daniel Roe
- Re: [AMBER] Problem with bonds in NAB Vladislav Sláma
- Re: [AMBER] MCPB.py Pengfei Li
- Re: [AMBER] Problem with bonds in NAB David A Case
- [AMBER] Error in running FEW calculations Miguel Rivera
- [AMBER] number of cpus in parallel GPU jobs Neha Gandhi
- Re: [AMBER] number of cpus in parallel GPU jobs Ross Walker
- [AMBER] AMBER FF for intrinsically disordered protein giulia palermo
- Re: [AMBER] AMBER FF for intrinsically disordered protein Neha Gandhi
Wednesday, 9 November 2016
- Re: [AMBER] Error in running FEW calculations Hannes Loeffler
- Re: [AMBER] Error in running FEW calculations Miguel Rivera
- Re: [AMBER] Error in running FEW calculations Hannes Loeffler
- Re: [AMBER] Error in running FEW calculations Miguel Rivera
- Re: [AMBER] Error in running FEW calculations Hannes Loeffler
- Re: [AMBER] enhanced sampling conformations by AMD Eric Lang
- [AMBER] log file in aMD Neha Gandhi
- Re: [AMBER] Uridine diphosphate (UDP) - tleap FyD
- [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories Eric Lang
- Re: [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories Nhai
- [AMBER] PCA trajectories give unrealistic structures Gulsevin,Alican
- Re: [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories Eric Lang
- Re: [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories David A Case
- Re: [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories Daniel Roe
- Re: [AMBER] PCA trajectories give unrealistic structures Daniel Roe
- [AMBER] integer limit for nstlim Neale, Christopher Andrew
- [AMBER] compute RESP charges asdda asa
- [AMBER] CUDA version for Amber14 Sofia Vasilakaki
- Re: [AMBER] integer limit for nstlim David A Case
Thursday, 10 November 2016
- Re: [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories William Lees
- Re: [AMBER] compute RESP charges Dr. Anselm Horn
- [AMBER] recompile Sander suite Ibrahim Said
- Re: [AMBER] recompile Sander suite Dr. Anselm Horn
- [AMBER] MCPB.py error in Step 2 Jon Mujika
- [AMBER] Constant pH charge set Fabrício Bracht
- [AMBER] Parameters for selenocysteine Paul Meister
- [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB Ruth Helena Tichauer
- Re: [AMBER] Constant pH charge set Jason Swails
- Re: [AMBER] CUDA version for Amber14 Ross Walker
- [AMBER] Problem with Parmed-generated chamber prmtop Marc van der Kamp
- Re: [AMBER] Parameters for selenocysteine David A Case
- Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB Gustavo Seabra
- Re: [AMBER] Parameters for selenocysteine David A Case
- Re: [AMBER] compute RESP charges asdda asa
- [AMBER] ambmask issue Aseel Bala
- Re: [AMBER] ambmask issue Hai Nguyen
- Re: [AMBER] ambmask issue Aseel Bala
- Re: [AMBER] Quenstions about pmemd.cuda.MPI Pengfei Li
- Re: [AMBER] Quenstions about pmemd.cuda.MPI Ross Walker
Friday, 11 November 2016
- [AMBER] cpptraj: RMSD vs Residue Number. Saman Yousuf ali
- Re: [AMBER] cpptraj: RMSD vs Residue Number. Daniel Roe
- [AMBER] GIST: convergence of the translational entropy term Sergey Samsonov
- [AMBER] Constraints Ol Sta
- Re: [AMBER] GIST: convergence of the translational entropy term Steven Ramsey
- [AMBER] NPT equilibration at constant pH with protonation states allowed to change Eric Lang
- Re: [AMBER] NPT equilibration at constant pH with protonation states allowed to change Jason Swails
- [AMBER] length of restraintmask Ignacio J. General
- Re: [AMBER] MCPB.py error in Step 2 Pengfei Li
- Re: [AMBER] GIST: convergence of the translational entropy term Tom Kurtzman
- [AMBER] MMGBSA decomposition analysis George Tzotzos
- Re: [AMBER] NPT equilibration at constant pH with protonation states allowed to change Eric Lang
- Re: [AMBER] MMGBSA decomposition analysis Carlos Simmerling
- Re: [AMBER] MMGBSA decomposition analysis George Tzotzos
- [AMBER] error in antechamber Nehad Elsalamouny
- Re: [AMBER] length of restraintmask David A Case
- Re: [AMBER] error in antechamber David A Case
Saturday, 12 November 2016
- [AMBER] Query regarding the MCPB.py workflow Abhi Acharya
Monday, 14 November 2016
- [AMBER] Generation of parameter files of transmembrane protein system via xleap Mahrukh Imtiaz
- Re: [AMBER] Generation of parameter files of transmembrane protein system via xleap Bill Ross
- [AMBER] dlpc membrane jojartb.jgypk.u-szeged.hu
- Re: [AMBER] NPT equilibration at constant pH with protonation states allowed to change Eric Lang
- Re: [AMBER] dlpc membrane Batuhan Kav
- Re: [AMBER] dlpc membrane jojartb.jgypk.u-szeged.hu
- Re: [AMBER] Generation of parameter files of transmembrane protein system via xleap David A Case
- Re: [AMBER] dlpc membrane David A Case
- Re: [AMBER] dlpc membrane jojartb.jgypk.u-szeged.hu
- [AMBER] Targeted molecular dynamics on GPU Sonia Ziada
- [AMBER] how to neutralize protein when using intrinsic water model Thakur, Abhishek
- [AMBER] Filename being truncated by pmemd.cuda Andreas Tosstorff
- Re: [AMBER] Filename being truncated by pmemd.cuda Adrian Roitberg
- Re: [AMBER] dlpc membrane David A Case
- Re: [AMBER] Filename being truncated by pmemd.cuda Andreas Tosstorff
- Re: [AMBER] how to neutralize protein when using intrinsic water model David A Case
- Re: [AMBER] dlpc membrane jojartb.jgypk.u-szeged.hu
- Re: [AMBER] dlpc membrane Nhai
- Re: [AMBER] dlpc membrane jojartb.jgypk.u-szeged.hu
- [AMBER] covalently bound ligand Ahsan Mohd
- Re: [AMBER] Filename being truncated by pmemd.cuda David A Case
- Re: [AMBER] Negative interaction energy between Sodium ions? Oliver Emil Skytte Glue
- Re: [AMBER] Negative interaction energy between Sodium ions? David Cerutti
- Re: [AMBER] dlpc membrane David A Case
- Re: [AMBER] covalently bound ligand David A Case
- Re: [AMBER] dlpc membrane jojartb.jgypk.u-szeged.hu
- [AMBER] Restraints not working, What Am I doing Wrong? The Cromicus Productions
- Re: [AMBER] covalently bound ligand FyD
Tuesday, 15 November 2016
- Re: [AMBER] Restraints not working, What Am I doing Wrong? Dr. Anselm Horn
- Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB Ruth Helena Tichauer
- [AMBER] Methylated adenine parameter Kshatresh Dutta Dubey
- Re: [AMBER] Umbrella simulation with an arbitrary bias potential diego.soler.uam.es
- Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB David A Case
- Re: [AMBER] Methylated adenine parameter David A Case
- Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB Ruth Helena Tichauer
- Re: [AMBER] Constraints David A Case
- Re: [AMBER] Constraints Roitberg,Adrian E
- Re: [AMBER] dlpc membrane David A Case
- [AMBER] simulating with "gbsa=1" on gpu give only 0.18ns per/day Thakur, Abhishek
- Re: [AMBER] simulating with "gbsa=1" on gpu give only 0.18ns per/day Adrian Roitberg
- Re: [AMBER] simulating with "gbsa=1" on gpu give only 0.18ns per/day Hai Nguyen
- [AMBER] Compatibility of Amber parameters for FF99 and FF14SB forcefields DmitryASuplatov
- Re: [AMBER] Compatibility of Amber parameters for FF99 and FF14SB forcefields Carlos Simmerling
- [AMBER] Help Constant pH MD calculations Tsibela German Tebello Mofokeng
- Re: [AMBER] simulating with "gbsa=1" on gpu give only 0.18ns per/day Thakur, Abhishek
- Re: [AMBER] Constraints Jason Swails
- Re: [AMBER] Help Constant pH MD calculations Jason Swails
- [AMBER] Energy decomposition of free energy profiles wjli
- Re: [AMBER] MD simulation by amber Hai Nguyen
- Re: [AMBER] mm_pbsa.pl error: Found unknown atflg DC Hai Nguyen
- Re: [AMBER] Problem with Parmed-generated chamber prmtop Hai Nguyen
- [AMBER] MM-GBSA calculation in temperature other than 298.15 K Atila Petrosian
Wednesday, 16 November 2016
- Re: [AMBER] Help Constant pH MD calculations Tsibela German Tebello Mofokeng
- Re: [AMBER] Query regarding the MCPB.py workflow Abhi Acharya
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Carlos Simmerling
- Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB Gustavo Seabra
- Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB Ruth Helena Tichauer
- Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB Hector A. Baldoni
- Re: [AMBER] MD simulation by amber David A Case
- [AMBER] GaMD patches to Amber 14 and PME's gridhi parameter Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] GaMD patches to Amber 14 and PME's gridhi parameter David A Case
- Re: [AMBER] GaMD patches to Amber 14 and PME's gridhi parameter Kasprzak, Wojciech (NIH/NCI) [C]
- [AMBER] HMassRepartition Thakur, Abhishek
- Re: [AMBER] HMassRepartition Elvis Martis
- Re: [AMBER] HMassRepartition David Cerutti
- Re: [AMBER] HMassRepartition Daniel Roe
- Re: [AMBER] HMassRepartition Thakur, Abhishek
- Re: [AMBER] HMassRepartition Thakur, Abhishek
- Re: [AMBER] HMassRepartition Elvis Martis
- Re: [AMBER] HMassRepartition David Cerutti
- Re: [AMBER] HMassRepartition Hai Nguyen
- Re: [AMBER] HMassRepartition Thakur, Abhishek
- Re: [AMBER] HMassRepartition Adrian Roitberg
- Re: [AMBER] HMassRepartition Adrian Roitberg
- [AMBER] compatibility Magno .
- Re: [AMBER] HMassRepartition Thakur, Abhishek
- Re: [AMBER] HMassRepartition Adrian Roitberg
- Re: [AMBER] HMassRepartition Thakur, Abhishek
- [AMBER] MD under external electric field Hector A. Baldoni
- [AMBER] ATP Parameters for ff14SB Stevens, David Ryan
- Re: [AMBER] ATP Parameters for ff14SB David Cerutti
- Re: [AMBER] MD under external electric field Charles Lin
- [AMBER] cpptraj RMSD calculation with mismatch residue numbers anu chandra
- Re: [AMBER] cpptraj RMSD calculation with mismatch residue numbers Nhai
- Re: [AMBER] Query regarding the MCPB.py workflow Pengfei Li
- Re: [AMBER] Query regarding the MCPB.py workflow Pengfei Li
- Re: [AMBER] ATP Parameters for ff14SB David A Case
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Atila Petrosian
Thursday, 17 November 2016
- [AMBER] Phosphoryated amino acids Beale, John
- Re: [AMBER] Phosphoryated amino acids Bill Ross
- Re: [AMBER] Phosphoryated amino acids Bill Ross
- Re: [AMBER] Phosphoryated amino acids Neha Gandhi
- Re: [AMBER] Phosphoryated amino acids Eiros Zamora, Juan
- [AMBER] No output_file during SMD with LCOD Ruth Helena Tichauer
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Carlos Simmerling
- [AMBER] Converting coordinate file generated into pdb format for nuparm ABHIJEET CHOWDHURY
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Atila Petrosian
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Carlos Simmerling
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Atila Petrosian
- Re: [AMBER] Phosphoryated amino acids David A Case
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Carlos Simmerling
- Re: [AMBER] Converting coordinate file generated into pdb format for nuparm David A Case
- [AMBER] Fwd: Normal Mode Analysis Imma Speciale
- Re: [AMBER] MD under external electric field Hector A. Baldoni
- Re: [AMBER] Converting coordinate file generated into pdb format for nuparm ABHIJEET CHOWDHURY
- Re: [AMBER] Converting coordinate file generated into pdb format for nuparm Nhai
- Re: [AMBER] Converting coordinate file generated into pdb format for nuparm ABHIJEET CHOWDHURY
- Re: [AMBER] Fwd: Normal Mode Analysis Nhai
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Daniel Roe
- Re: [AMBER] No output_file during SMD with LCOD Feng Pan
- [AMBER] creating parameters for integrins Tsibela German Tebello Mofokeng
- [AMBER] ImportError: Could not import Amber Python modules Thakur, Abhishek
- Re: [AMBER] creating parameters for integrins Nhai
- Re: [AMBER] ImportError: Could not import Amber Python modules Nhai
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Jason Swails
- [AMBER] ambmask issue Aseel Bala
- [AMBER] extracting velocities from rst7 file giulia palermo
- Re: [AMBER] ImportError: Could not import Amber Python modules Thakur, Abhishek
- Re: [AMBER] ImportError: Could not import Amber Python modules Nhai
- Re: [AMBER] ImportError: Could not import Amber Python modules Thakur, Abhishek
- [AMBER] Issue with addAtomType: Syntax Error Korey M Reid
- Re: [AMBER] Issue with addAtomType: Syntax Error Bill Ross
- Re: [AMBER] ImportError: Could not import Amber Python modules David A Case
- Re: [AMBER] ImportError: Could not import Amber Python modules Daniel Roe
- Re: [AMBER] MD under external electric field Charles Lin
- Re: [AMBER] ImportError: Could not import Amber Python modules Thakur, Abhishek
- Re: [AMBER] extracting velocities from rst7 file Hai Nguyen
- Re: [AMBER] extracting velocities from rst7 file Daniel Roe
- Re: [AMBER] Issue with addAtomType: Syntax Error Korey M Reid
- Re: [AMBER] Issue with addAtomType: Syntax Error Bill Ross
- Re: [AMBER] ImportError: Could not import Amber Python modules Jason Swails
- Re: [AMBER] ImportError: Could not import Amber Python modules Niel Henriksen
- Re: [AMBER] extracting velocities from rst7 file giulia palermo
- Re: [AMBER] extracting velocities from rst7 file Nhai
- Re: [AMBER] extracting velocities from rst7 file Daniel Roe
- Re: [AMBER] creating parameters for integrins Tsibela German Tebello Mofokeng
Friday, 18 November 2016
- Re: [AMBER] cpptraj RMSD calculation with mismatch residue numbers anu chandra
- Re: [AMBER] ImportError: Could not import Amber Python modules David A Case
- Re: [AMBER] ImportError: Could not import Amber Python modules David A Case
- Re: [AMBER] Issue with addAtomType: Syntax Error David A Case
- Re: [AMBER] No output_file during SMD with LCOD Ruth Helena Tichauer
- Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB Ruth Helena Tichauer
- [AMBER] strange format of .rst file Thakur, Abhishek
- Re: [AMBER] strange format of .rst file Daniel Roe
- Re: [AMBER] strange format of .rst file Thakur, Abhishek
- Re: [AMBER] strange format of .rst file Jason Swails
- [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) The Cromicus Productions
- Re: [AMBER] Restraints not working, What Am I doing Wrong? The Cromicus Productions
- Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) Hai Nguyen
- Re: [AMBER] Problem with Parmed-generated chamber prmtop Jason Swails
- [AMBER] Converting a PDB Collection to a NetCDF trajectory Dmitry Suplatov
- Re: [AMBER] Converting a PDB Collection to a NetCDF trajectory Hai Nguyen
- Re: [AMBER] Converting a PDB Collection to a NetCDF trajectory Christina Bergonzo
- Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) The Cromicus Productions
- Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) Hai Nguyen
- Re: [AMBER] Issue with addAtomType: Syntax Error Korey M Reid
- Re: [AMBER] Problem with Parmed-generated chamber prmtop Marc van der Kamp
- Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) The Cromicus Productions
- Re: [AMBER] Problem with Parmed-generated chamber prmtop Jason Swails
- Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) Hai Nguyen
- Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) The Cromicus Productions
- [AMBER] generated correct inputfiles(.iprmtop and .inpcrd ) files 杨满意
Saturday, 19 November 2016
- [AMBER] TUTORIAL B5: Simulating the Green Fluorescent Protein -PREPGEN Error Taylor, Miles
- Re: [AMBER] Query regarding the MCPB.py workflow Abhi Acharya
Sunday, 20 November 2016
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Atila Petrosian
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Daniel Roe
- Re: [AMBER] TUTORIAL B5: Simulating the Green Fluorescent Protein -PREPGEN Error Brent Krueger
- [AMBER] How to change the dielectric constant in the electrostatic energy term? 冯国强
- Re: [AMBER] How to change the dielectric constant in the electrostatic energy term? David A Case
- [AMBER] The parameters for the fully protonated phosphate group jinfeng liu
- Re: [AMBER] The parameters for the fully protonated phosphate group David Cerutti
- Re: [AMBER] The parameters for the fully protonated phosphate group Dd H
Monday, 21 November 2016
- Re: [AMBER] The parameters for the fully protonated phosphate group David A Case
- Re: [AMBER] TUTORIAL B5: Simulating the Green Fluorescent Protein -PREPGEN Error David A Case
- [AMBER] MMPBSA Calculation Preeti Pandey
- Re: [AMBER] The parameters for the fully protonated phosphate group David Cerutti
- [AMBER] Lifetime Analysis in cpptraj MOHD HOMAIDUR RAHMAN
- [AMBER] Convert prm into prmtop - from NAMD to AMBER The Cromicus Productions
- Re: [AMBER] Convert prm into prmtop - from NAMD to AMBER Hai Nguyen
- Re: [AMBER] Convert prm into prmtop - from NAMD to AMBER The Cromicus Productions
- Re: [AMBER] Convert prm into prmtop - from NAMD to AMBER Amy Rice
- Re: [AMBER] Convert prm into prmtop - from NAMD to AMBER The Cromicus Productions
- [AMBER] cap the 5' phosphate of a RNA Mohaddeseh Habibzadeh
- [AMBER] 20161121141138.GE88784.scarletmail.rutgers.edu Taylor, Miles
- Re: [AMBER] 20161121141138.GE88784.scarletmail.rutgers.edu David Cerutti
- [AMBER] implicit water model in aMD Thakur, Abhishek
- Re: [AMBER] Query regarding the MCPB.py workflow Pengfei Li
- [AMBER] creating 5' phosphate groups David A Case
- [AMBER] [Amber] Calculating Normal Modes with Restrictions The Cromicus Productions
Tuesday, 22 November 2016
- Re: [AMBER] AMBER Digest, Vol 1763, Issue 1 冯国强
- [AMBER] Protein path error Arthi Venkat
- Re: [AMBER] Protein path error Elvis Martis
- Re: [AMBER] Protein path error Arthi Venkat
- Re: [AMBER] Protein path error Elvis Martis
- Re: [AMBER] Fwd: Normal Mode Analysis Imma Speciale
- Re: [AMBER] Protein path error Arthi Venkat
- Re: [AMBER] Protein path error Elvis Martis
- Re: [AMBER] [Amber] Calculating Normal Modes with Restrictions David A Case
- Re: [AMBER] Fwd: Normal Mode Analysis David A Case
- Re: [AMBER] generated correct inputfiles(.iprmtop and .inpcrd ) files David A Case
- Re: [AMBER] Fwd: Normal Mode Analysis The Cromicus Productions
- Re: [AMBER] [Amber] Calculating Normal Modes with Restrictions The Cromicus Productions
- Re: [AMBER] Fwd: Normal Mode Analysis Imma Speciale
- Re: [AMBER] Lifetime Analysis in cpptraj Daniel Roe
- Re: [AMBER] [Amber] Calculating Normal Modes with Restrictions The Cromicus Productions
- [AMBER] Modes associated to the principal components? The Cromicus Productions
- [AMBER] Could not find enough velocities in .rst Ruth Helena Tichauer
- Re: [AMBER] Modes associated to the principal components? Jason Swails
- Re: [AMBER] Could not find enough velocities in .rst Daniel Roe
- Re: [AMBER] Modes associated to the principal components? The Cromicus Productions
- Re: [AMBER] Modes associated to the principal components? David A Case
- [AMBER] DIfferences between thermostats Markowska
- Re: [AMBER] DIfferences between thermostats Gustavo Seabra
- Re: [AMBER] DIfferences between thermostats Geoffrey Gray
- Re: [AMBER] DIfferences between thermostats Markowska
- Re: [AMBER] DIfferences between thermostats Gustavo Seabra
- [AMBER] is it possible to run aMD in implicit water model? Thakur, Abhishek
- Re: [AMBER] is it possible to run aMD in implicit water model? Pengfei Li
- Re: [AMBER] DIfferences between thermostats Geoffrey Gray
- Re: [AMBER] is it possible to run aMD in implicit water model? Thakur, Abhishek
- Re: [AMBER] DIfferences between thermostats David Cerutti
- Re: [AMBER] DIfferences between thermostats Adrian Roitberg
- Re: [AMBER] DIfferences between thermostats David Cerutti
- [AMBER] Paramfit for multiple molecules Sven Hackbusch
- Re: [AMBER] is it possible to run aMD in implicit water model? Pengfei Li
- [AMBER] How to generated correct inputfiles(.iprmtop and .inpcrd ) files 杨满意
- Re: [AMBER] DIfferences between thermostats David A Case
- Re: [AMBER] is it possible to run aMD in implicit water model? Thakur, Abhishek
- [AMBER] simulation running error. Saman Yousuf ali
- Re: [AMBER] simulation running error. Elvis Martis
- Re: [AMBER] simulation running error. Saman Yousuf ali
- Re: [AMBER] simulation running error. Bill Ross
- Re: [AMBER] simulation running error. Saman Yousuf ali
Wednesday, 23 November 2016
- Re: [AMBER] DIfferences between thermostats Markowska
- Re: [AMBER] Could not find enough velocities in .rst Ruth Helena Tichauer
- [AMBER] rmsf problem Sepideh Jafari
- Re: [AMBER] rmsf problem Elvis Martis
- [AMBER] Error, charge not integral Fabrício Bracht
- Re: [AMBER] Error, charge not integral Fabrício Bracht
- Re: [AMBER] Error, charge not integral Bill Ross
- Re: [AMBER] Error, charge not integral Lachele Foley
- Re: [AMBER] Error, charge not integral Fabrício Bracht
- Re: [AMBER] rmsf problem Eiros Zamora, Juan
- Re: [AMBER] Could not find enough velocities in .rst Daniel Roe
- Re: [AMBER] rmsf problem Daniel Roe
- Re: [AMBER] Could not find enough velocities in .rst Ruth Helena Tichauer
- [AMBER] aMD with dt=0.004 Thakur, Abhishek
- [AMBER] About multiconformations RESP fitting Marion, Antoine
- Re: [AMBER] aMD with dt=0.004 Nhai
- Re: [AMBER] DIfferences between thermostats David Cerutti
- Re: [AMBER] DIfferences between thermostats Marc van der Kamp
- [AMBER] 20161121141138.GE88784.scarletmail.rutgers.edu Taylor, Miles
- Re: [AMBER] DIfferences between thermostats Nhai
- Re: [AMBER] About multiconformations RESP fitting David Cerutti
- Re: [AMBER] DIfferences between thermostats Gustavo Seabra
- Re: [AMBER] Problem with Parmed-generated chamber prmtop Jason Swails
- Re: [AMBER] About multiconformations RESP fitting Marion, Antoine
- Re: [AMBER] About multiconformations RESP fitting David Cerutti
- [AMBER] more on the Berendsen thermostat David A Case
- Re: [AMBER] more on the Berendsen thermostat Adrian Roitberg
- Re: [AMBER] DIfferences between thermostats Markowska
- Re: [AMBER] more on the Berendsen thermostat Markowska
- Re: [AMBER] DIfferences between thermostats Gustavo Seabra
- Re: [AMBER] DIfferences between thermostats Markowska
- Re: [AMBER] DIfferences between thermostats David Cerutti
- Re: [AMBER] DIfferences between thermostats Markowska
- [AMBER] Hydrophobic and covalent interactions bond length and stability muhammad tahir ayub
- Re: [AMBER] Distorsion in water box size and shape Mahrukh Imtiaz
Thursday, 24 November 2016
- Re: [AMBER] About multiconformations RESP fitting Marion, Antoine
- Re: [AMBER] About multiconformations RESP fitting FyD
- Re: [AMBER] Problem with Parmed-generated chamber prmtop Marc van der Kamp
- [AMBER] Optimal values for harm and output_freq in SMD Ruth Helena Tichauer
- Re: [AMBER] DIfferences between thermostats Gustavo Seabra
- Re: [AMBER] DIfferences between thermostats Markowska
- Re: [AMBER] DIfferences between thermostats Gustavo Seabra
- Re: [AMBER] About multiconformations RESP fitting Marion, Antoine
- Re: [AMBER] Problem with bonds in NAB Vladislav Sláma
- Re: [AMBER] Optimal values for harm and output_freq in SMD Feng Pan
- Re: [AMBER] Problem with bonds in NAB David A Case
Friday, 25 November 2016
- Re: [AMBER] About multiconformations RESP fitting FyD
- Re: [AMBER] About multiconformations RESP fitting Marion, Antoine
- [AMBER] GlcNAc-UDP problem with frcmod file Sonia Romero
- [AMBER] Problem to submit a pH-REMD on a GPU node Yong Wang
- [AMBER] Extract temperature of a subsytem diego.soler.uam.es
- Re: [AMBER] GlcNAc-UDP problem with frcmod file Hannes Loeffler
- Re: [AMBER] Optimal values for harm and output_freq in SMD Ruth Helena Tichauer
- [AMBER] Dynamic at high temperature Imma Speciale
- Re: [AMBER] Wierd line in amber-TI output Files Thomas Fox
- Re: [AMBER] Extract temperature of a subsytem Gustavo Seabra
- Re: [AMBER] Dynamic at high temperature David A Case
- Re: [AMBER] Extract temperature of a subsytem diego.soler.uam.es
- Re: [AMBER] Extract temperature of a subsytem Nhai
- Re: [AMBER] Extract temperature of a subsytem Daniel Roe
- Re: [AMBER] Problem to submit a pH-REMD on a GPU node Ross Walker
- [AMBER] instal aamber "mpich2" Sepideh Jafari
- Re: [AMBER] instal aamber "mpich2" Nhai
- [AMBER] Tools for calculation of interaction energy Andrew Bostick
- Re: [AMBER] instal aamber "mpich2" Sepideh Jafari
- Re: [AMBER] Dynamic at high temperature Carlos Simmerling
- Re: [AMBER] instal aamber "mpich2" David A Case
- Re: [AMBER] Tools for calculation of interaction energy Nhai
- [AMBER] Convert mdcrd files into pbd files The Cromicus Productions
- Re: [AMBER] Convert mdcrd files into pbd files Nhai
Saturday, 26 November 2016
- [AMBER] Obtaining infrared/Raman spectra The Cromicus Productions
- [AMBER] MCPB.py and MMPBSA issue 庄灿波
- Re: [AMBER] Obtaining infrared/Raman spectra case
- [AMBER] recipe for target "parallel" failed Mohaddeseh Habibzadeh
- Re: [AMBER] recipe for target "parallel" failed Elvis Martis
- Re: [AMBER] recipe for target "parallel" failed Mohaddeseh Habibzadeh
- Re: [AMBER] Obtaining infrared/Raman spectra Brent Krueger
- Re: [AMBER] recipe for target "parallel" failed David A Case
- [AMBER] How to create the .off/.lib file of the equilibrated non-aqueous solvent box? Yew Mun Yip
- Re: [AMBER] recipe for target "parallel" failed Mohaddeseh Habibzadeh
- [AMBER] NAB input file containing first and second structure of RNA Mohaddeseh Habibzadeh
- Re: [AMBER] recipe for target "parallel" failed Mohaddeseh Habibzadeh
- Re: [AMBER] recipe for target "parallel" failed Elvis Martis
Sunday, 27 November 2016
- Re: [AMBER] recipe for target "parallel" failed Mohaddeseh Habibzadeh
- Re: [AMBER] recipe for target "parallel" failed Elvis Martis
- Re: [AMBER] creating 5' phosphate groups Mohaddeseh Habibzadeh
- Re: [AMBER] creating 5' phosphate groups David A Case
- Re: [AMBER] NAB input file containing first and second structure of RNA David A Case
- Re: [AMBER] NAB input file containing first and second structure of RNA Mohaddeseh Habibzadeh
- Re: [AMBER] creating 5' phosphate groups Mohaddeseh Habibzadeh
- Re: [AMBER] Convert mdcrd files into pbd files Daniel Roe
- Re: [AMBER] NAB input file containing first and second structure of RNA David A Case
- Re: [AMBER] How to create the .off/.lib file of the equilibrated non-aqueous solvent box? David A Case
- [AMBER] Regarding integration of my code with CPPTRAJ Nikhil Chowdary
- [AMBER] AMBER Materials modelling- periodic image Neha Gandhi
- Re: [AMBER] Regarding integration of my code with CPPTRAJ Hai Nguyen
Monday, 28 November 2016
- [AMBER] cudaMemcpyToSymbol Error cuiyinglukitty
- Re: [AMBER] cudaMemcpyToSymbol Error Charles Lin
- Re: [AMBER] cudaMemcpyToSymbol Error Charles Lin
- Re: [AMBER] NAB input file containing first and second structure of RNA Mohaddeseh Habibzadeh
- [AMBER] Questions concerning charges calculated by antechamber Andreas Gavrielides
- Re: [AMBER] Regarding integration of my code with CPPTRAJ Daniel Roe
- Re: [AMBER] Questions concerning charges calculated by antechamber Daniel Roe
- Re: [AMBER] cudaMemcpyToSymbol Error Ross Walker
- [AMBER] solvate box of long length and short width Lara rajam
- [AMBER] Etot = ************** with dtt=0.004 Thakur, Abhishek
- Re: [AMBER] Etot = ************** with dtt=0.004 Carlos Simmerling
- Re: [AMBER] Etot = ************** with dtt=0.004 Thakur, Abhishek
- Re: [AMBER] Etot = ************** with dtt=0.004 Roitberg,Adrian E
- Re: [AMBER] Etot = ************** with dtt=0.004 Thakur, Abhishek
- Re: [AMBER] Etot = ************** with dtt=0.004 Thakur, Abhishek
- Re: [AMBER] Etot = ************** with dtt=0.004 Carlos Simmerling
- Re: [AMBER] Etot = ************** with dtt=0.004 Thakur, Abhishek
- Re: [AMBER] Etot = ************** with dtt=0.004 Nhai
- [AMBER] MM-GBSA calculation in temperature other than 298 K Atila Petrosian
- Re: [AMBER] MM-GBSA calculation in temperature other than 298 K Hai Nguyen
- Re: [AMBER] solvate box of long length and short width David A Case
- Re: [AMBER] GlcNAc-UDP problem with frcmod file David A Case
- Re: [AMBER] Etot = ************** with dtt=0.004 Ross Walker
- Re: [AMBER] solvate box of long length and short width Lara rajam
- [AMBER] RMSD for two different MDs Haining Liu
- [AMBER] Fw: Problems with imaging Mark Waterhouse [RPG]
- Re: [AMBER] MCPB.py and MMPBSA issue Pengfei Li
- Re: [AMBER] AMBER Materials modelling- periodic image Pengfei Li
- Re: [AMBER] RMSD for two different MDs Thakur, Abhishek
- Re: [AMBER] RMSD for two different MDs Adrian Roitberg
- Re: [AMBER] RMSD for two different MDs David Cerutti
- Re: [AMBER] Paramfit for multiple molecules Robin Betz
- Re: [AMBER] Optimal values for harm and output_freq in SMD Feng Pan
- Re: [AMBER] GlcNAc-UDP problem with frcmod file Lachele Foley
Tuesday, 29 November 2016
- Re: [AMBER] RMSD for two different MDs Daniel Roe
- Re: [AMBER] Fw: Problems with imaging Daniel Roe
- Re: [AMBER] Optimal values for harm and output_freq in SMD Ruth Helena Tichauer
- Re: [AMBER] MCPB.py and MMPBSA issue Jason Swails
- [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Brian Radak
- Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Daniel Roe
- Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Brian Radak
- Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Daniel Roe
- Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Brian Radak
- Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Daniel Roe
- Re: [AMBER] Optimal values for harm and output_freq in SMD Feng Pan
- [AMBER] Error for copper atom type Shreeramesh
- Re: [AMBER] Error for copper atom type Elvis Martis
Wednesday, 30 November 2016
- Re: [AMBER] Fw: Problems with imaging Mark Waterhouse [RPG]
- Re: [AMBER] Optimal values for harm and output_freq in SMD Ruth Helena Tichauer
- [AMBER] Force field files for ff99IDPs barsha bharadwaz
- Re: [AMBER] Force field files for ff99IDPs Carlos Simmerling
- [AMBER] Issue with the gaff parameters for "nh" atom type Prajwal Nandekar
- [AMBER] question about calculated density in sander output file amaury paquet
- [AMBER] selection of the residues when using MM-GBSA Hyun
- Re: [AMBER] Fw: Problems with imaging Daniel Roe
- Re: [AMBER] Issue with the gaff parameters for "nh" atom type Hirdesh Kumar
- Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Daniel Roe
- Re: [AMBER] question about calculated density in sander output file David A Case
- Re: [AMBER] cpptraj RMSD calculation with mismatch residue numbers Daniel Roe
- Re: [AMBER] selection of the residues when using MM-GBSA Jason Swails
- [AMBER] mdfil: Error unknown flag: pdb_wat.prmtop Aishani Prem
- Re: [AMBER] mdfil: Error unknown flag: pdb_wat.prmtop Hai Nguyen

Last message date: Wed Nov 30 2016 - 16:00:03 PST
Archived on: Mon Nov 25 2024 - 05:55:20 PST

Amber Archive Nov 2016 by date