Amber Archive Sep 2015: by date

Tuesday, 1 September 2015
- Re: [AMBER] Non-equilibrium pulling with plane-point restraints achim.sandmann.chemie.stud.uni-erlangen.de
- [AMBER] MMPBSA error - start frame (1) > total frames (0) Sangeetha B
- Re: [AMBER] MMPBSA error - start frame (1) > total frames (0) Daniel Roe
- [AMBER] KeyError: 4018 Sushi Shilpa
Wednesday, 2 September 2015
- [AMBER] lifetime analysis loic etheve
- [AMBER] lifetime analysis loic etheve
- Re: [AMBER] lifetime analysis Daniel Roe
- Re: [AMBER] lifetime analysis loic etheve
- Re: [AMBER] lifetime analysis Daniel Roe
- Re: [AMBER] lifetime analysis loic etheve
- [AMBER] Amber14 Update 13 fails. Oliver Grant
- Re: [AMBER] Amber14 Update 13 fails. Jason Swails
- [AMBER] error in GPU during equilibration Lara rajam
- Re: [AMBER] error in GPU during equilibration David A Case
- Re: [AMBER] error in GPU during equilibration Lara rajam
- Re: [AMBER] error in GPU during equilibration Ross Walker
- Re: [AMBER] error in GPU during equilibration Ross Walker
- [AMBER] Different result before and after AUTOIMAGE from CPPTRAJ? Eg eh
- Re: [AMBER] Different result before and after AUTOIMAGE from CPPTRAJ? Jason Swails
- Re: [AMBER] error in GPU during equilibration Lara rajam
- Re: [AMBER] error in GPU during equilibration Ross Walker
- Re: [AMBER] error in GPU during equilibration Lara rajam
- Re: [AMBER] KeyError: 4018 Pengfei Li
Thursday, 3 September 2015
- Re: [AMBER] job submission in RED FyD
- Re: [AMBER] hpc error Damiano Spadoni
- Re: [AMBER] hpc error Jason Swails
- [AMBER] RESP charge fitting CHAMI F.
- Re: [AMBER] RESP charge fitting David A Case
- [AMBER] Trouble running Thermodynamic Integration in Amber14 with pmemd. Timothy Christopher Schutt
- Re: [AMBER] Trouble running Thermodynamic Integration in Amber14 with pmemd. David A Case
- Re: [AMBER] RESP charge fitting FyD
- Re: [AMBER] Trouble running Thermodynamic Integration in Amber14 with pmemd. hannes.loeffler.stfc.ac.uk
Friday, 4 September 2015
- [AMBER] MMPBSA error sunita gupta
- Re: [AMBER] MMPBSA error Jason Swails
- [AMBER] chirality.c Aronica, Pietro
- Re: [AMBER] Trouble running Thermodynamic Integration in Amber14 with pmemd. Timothy Christopher Schutt
- Re: [AMBER] Trouble running Thermodynamic Integration in Amber14 with pmemd. hannes.loeffler.stfc.ac.uk
- [AMBER] mmpbsa with Iodine problems 21428087.zju.edu.cn
Saturday, 5 September 2015
- Re: [AMBER] chirality.c David A Case
- [AMBER] gpu run Lara rajam
- Re: [AMBER] mmpbsa with Iodine problems Kenneth Huang
- Re: [AMBER] gpu run Kenneth Huang
Sunday, 6 September 2015
- Re: [AMBER] gpu run Ross Walker
- Re: [AMBER] gpu run Lara rajam
- Re: [AMBER] gpu run Jason Swails
- [AMBER] MMPBSA is not performing Asma Abro 28-FBAS/MSBI/F09
Monday, 7 September 2015
- Re: [AMBER] MMPBSA is not performing Jason Swails
- Re: [AMBER] Trouble running Thermodynamic Integration in Amber14 with pmemd. Timothy Christopher Schutt
- [AMBER] Multiplicity in QM/MM calculations Kshatresh Dutta Dubey
- [AMBER] Parameters for benzene sulfonamide Jovanovic, Srdan
- Re: [AMBER] Multiplicity in QM/MM calculations Jason Swails
- Re: [AMBER] Trouble running Thermodynamic Integration in Amber14 with pmemd. Jason Swails
- Re: [AMBER] closest command in cpptraj Joseph Baker
- Re: [AMBER] Regarding AmberTool 14 installation Setyanto Md
- Re: [AMBER] Regarding AmberTool 14 installation MOHD HOMAIDUR RAHMAN
- Re: [AMBER] Regarding AmberTool 14 installation Setyanto Md
Tuesday, 8 September 2015
- Re: [AMBER] MMPBSA is not performing Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] Regarding AmberTool 14 installation MOHD HOMAIDUR RAHMAN
- [AMBER] REMD to sample the conformational space of a defined part of the system Sergey Samsonov
- Re: [AMBER] MMPBSA is not performing Aleksandra Skoric
- Re: [AMBER] MMPBSA is not performing asma.msbi28.iiu.edu.pk
- Re: [AMBER] Parameters for benzene sulfonamide Karl Kirschner
- Re: [AMBER] MMPBSA is not performing Aleksandra Skoric
- Re: [AMBER] MMPBSA is not performing asma.msbi28.iiu.edu.pk
- Re: [AMBER] Regarding AmberTool 14 installation Setyanto Md
- Re: [AMBER] MMPBSA is not performing Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] MMPBSA is not performing Aleksandra Skoric
- Re: [AMBER] MMPBSA is not performing Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] MMPBSA is not performing Aleksandra Skoric
- Re: [AMBER] REMD to sample the conformational space of a defined part of the system Jason Swails
- Re: [AMBER] MMPBSA is not performing asma.msbi28.iiu.edu.pk
- [AMBER] Amber15 compiler error 'undefined reference to `fftw_plan_dft_r2c_3d'' with Cygwin Nigel Palmer
- Re: [AMBER] MMPBSA is not performing Jason Swails
- Re: [AMBER] Amber15 compiler error 'undefined reference to `fftw_plan_dft_r2c_3d'' with Cygwin Jason Swails
- Re: [AMBER] Amber15 compiler error 'undefined reference to `fftw_plan_dft_r2c_3d'' with Cygwin Nigel Palmer
- Re: [AMBER] chirality.c Aronica, Pietro
- Re: [AMBER] REMD to sample the conformational space of a defined part of the system Sergey Samsonov
- Re: [AMBER] MMPBSA is not performing asma.msbi28.iiu.edu.pk
- [AMBER] index and sort order in prmtop Hannes Loeffler
- [AMBER] watershell cpptraj question Travis Hughes
- [AMBER] Problem compiling cpptraj with openmp Marc van der Kamp
- Re: [AMBER] Problem compiling cpptraj with openmp Daniel Roe
- Re: [AMBER] Problem compiling cpptraj with openmp Hannes Loeffler
- Re: [AMBER] closest command in cpptraj Daniel Roe
- Re: [AMBER] watershell cpptraj question Daniel Roe
- Re: [AMBER] Problem compiling cpptraj with openmp Marc van der Kamp
- Re: [AMBER] REMD to sample the conformational space of a defined part of the system Jason Swails
- Re: [AMBER] index and sort order in prmtop Jason Swails
- [AMBER] ParmEd problem: LJ12_6_4Error: Could not find parameters for ATOM_TYPE CX Karolina Markowska
Wednesday, 9 September 2015
- [AMBER] Fw: important Do Yong Kim
- [AMBER] Contact map residues Neha Gandhi
- [AMBER] Cphmd Arjun Sharma
- [AMBER] Changing font size with mdout_analyzer.py Krantzman, Kristin D
- Re: [AMBER] ParmEd problem: LJ12_6_4Error: Could not find parameters for ATOM_TYPE CX Jason Swails
- Re: [AMBER] Changing font size with mdout_analyzer.py Jason Swails
- Re: [AMBER] Cphmd Jason Swails
- [AMBER] [parmed.py] chemistry.exceptions.AmberParmError loading topology file Eiros Zamora, Juan
- Re: [AMBER] ParmEd problem: LJ12_6_4Error: Could not find parameters for ATOM_TYPE CX Karolina Markowska
- [AMBER] QM/MM Equilibration Errors Brittany Boykin
- Re: [AMBER] [parmed.py] chemistry.exceptions.AmberParmError loading topology file Jason Swails
Thursday, 10 September 2015
- [AMBER] cpptraj script for average 3D protein structure? Michael Shokhen
- Re: [AMBER] cpptraj script for average 3D protein structure? Repic Matej
- [AMBER] several peptides in my input can be identified by cpptraj? Fabian gmail
- Re: [AMBER] cpptraj script for average 3D protein structure? Michael Shokhen
- Re: [AMBER] cpptraj script for average 3D protein structure? Eiros Zamora, Juan
- Re: [AMBER] [parmed.py] chemistry.exceptions.AmberParmError loading topology file Eiros Zamora, Juan
- Re: [AMBER] [parmed.py] chemistry.exceptions.AmberParmError loading topology file Jason Swails
- Re: [AMBER] cpptraj script for average 3D protein structure? Michael Shokhen
- Re: [AMBER] QM/MM Equilibration Errors David A Case
- [AMBER] xmgrace in microsoft Martina Devi
- Re: [AMBER] xmgrace in microsoft Jason Swails
- Re: [AMBER] xmgrace in microsoft David A Case
- Re: [AMBER] xmgrace in microsoft Martina Devi
- [AMBER] pca Lara rajam
- [AMBER] setting a box mohammad r
- Re: [AMBER] setting a box David A Case
- Re: [AMBER] setting a box mohammad r
- [AMBER] HPC Sofia Vasilakaki
- Re: [AMBER] HPC Ross Walker
- [AMBER] MCPB problem Kshatresh Dutta Dubey
- Re: [AMBER] HPC Sofia Vasilakaki
Friday, 11 September 2015
- Re: [AMBER] REMD to sample the conformational space of a defined part of the system Sergey Samsonov
- [AMBER] keep residue numbering? Albert
- Re: [AMBER] [parmed.py] chemistry.exceptions.AmberParmError loading topology file Juan Eiros Zamora
- Re: [AMBER] REMD to sample the conformational space of a defined part of the system Carlos Simmerling
- Re: [AMBER] REMD to sample the conformational space of a defined part of the system Sergey Samsonov
- [AMBER] limit exceeded and high temperature Ruth Helena Tichauer
- Re: [AMBER] keep residue numbering? David A Case
- Re: [AMBER] limit exceeded and high temperature Jason Swails
- Re: [AMBER] limit exceeded and high temperature Ruth Helena Tichauer
- Re: [AMBER] limit exceeded and high temperature Ross Walker
- Re: [AMBER] MCPB problem Pengfei Li
- Re: [AMBER] limit exceeded and high temperature Ruth Helena Tichauer
- Re: [AMBER] MCPB problem Kshatresh Dutta Dubey
- Re: [AMBER] MCPB problem Pengfei Li
- Re: [AMBER] MCPB problem Kshatresh Dutta Dubey
- [AMBER] Parameterization empirical method Marcelo Andrade Chagas
- [AMBER] Addition of single water molecules Eric Berquist
- Re: [AMBER] Addition of single water molecules Jason Swails
- [AMBER] CpHMD of Succinic Acid Rahul Ramesh
- Re: [AMBER] xmgrace in microsoft Luciano Costa
Saturday, 12 September 2015
- Re: [AMBER] MCPB problem Kshatresh Dutta Dubey
- [AMBER] FW: No output Damiano Spadoni
- Re: [AMBER] No output Ross Walker
- Re: [AMBER] MCPB problem Pengfei Li
- Re: [AMBER] MCPB problem Kshatresh Dutta Dubey
- Re: [AMBER] CpHMD of Succinic Acid Jason Swails
- Re: [AMBER] MCPB problem Kshatresh Dutta Dubey
- Re: [AMBER] No output Jason Swails
Sunday, 13 September 2015
- [AMBER] Testing the mail server George Tzotzos
- [AMBER] Proper Insertion of Covalently Bound Unit in Helical Structure Robert Molt
- [AMBER] What is wrong with the minimization? Huggins, Esther, C
- Re: [AMBER] Proper Insertion of Covalently Bound Unit in Helical Structure David A Case
- Re: [AMBER] What is wrong with the minimization? David A Case
Monday, 14 September 2015
- [AMBER] Simulation stops without errors Bala subramanian
- Re: [AMBER] limit exceeded and high temperature Ruth Helena Tichauer
- [AMBER] Paramfit issues David Poole
- Re: [AMBER] No output Damiano Spadoni
- Re: [AMBER] No output Jason Swails
- Re: [AMBER] Simulation stops without errors Jason Swails
- Re: [AMBER] What is wrong with the minimization? Huggins, Esther, C
- [AMBER] Parmed crash Mykola Dimura
- Re: [AMBER] What is wrong with the minimization? Jason Swails
- Re: [AMBER] Parmed crash Jason Swails
- Re: [AMBER] What is wrong with the minimization? Huggins, Esther, C
- Re: [AMBER] MCPB problem Pengfei Li
- Re: [AMBER] What is wrong with the minimization? Jason Swails
- Re: [AMBER] Parmed crash Mykola Dimura
- Re: [AMBER] Parmed crash Jason Swails
- Re: [AMBER] MCPB problem Kshatresh Dutta Dubey
- Re: [AMBER] Proper Insertion of Covalently Bound Unit in Helical Structure Dr. Robert Molt Jr.
- Re: [AMBER] Proper Insertion of Covalently Bound Unit in Helical Structure Robert Molt
- Re: [AMBER] MCPB problem Pengfei Li
- Re: [AMBER] What is wrong with the minimization? David A Case
- Re: [AMBER] Paramfit issues Robin Betz
- Re: [AMBER] Proper Insertion of Covalently Bound Unit in Helical Structure David A Case
- [AMBER] mmpbsa error Lara rajam
- [AMBER] Regarding Simulations of Ionic Liquids on GPU MOHD HOMAIDUR RAHMAN
- [AMBER] A question on binding free energy decomposition output wliu
Tuesday, 15 September 2015
- Re: [AMBER] A question on binding free energy decomposition output Sofia Vasilakaki
- Re: [AMBER] Regarding Simulations of Ionic Liquids on GPU David A Case
- [AMBER] query ankita mehta
- [AMBER] query Kenneth Huang
- [AMBER] sqm Sofia Vasilakaki
- Re: [AMBER] sqm Hannes Loeffler
- Re: [AMBER] mmpbsa error Jason Swails
- Re: [AMBER] sqm Sofia Vasilakaki
- Re: [AMBER] A question on binding free energy decomposition output Jason Swails
- Re: [AMBER] sqm Jason Swails
- Re: [AMBER] sqm Hannes Loeffler
- [AMBER] Has anyone tried VMD in the second step of tutorial A1? Xing
- [AMBER] vlimit exceeded and high temperature Ruth Helena Tichauer
- Re: [AMBER] mmpbsa error Lara rajam
- [AMBER] cyclic peptides and bond command in leap Jonathan Gough
- Re: [AMBER] mmpbsa error Jason Swails
- Re: [AMBER] query David A Case
- Re: [AMBER] sqm David A Case
- [AMBER] Antechamber error Kalenkiewicz, Andrew (NIH/NICHD) [F]
- Re: [AMBER] vlimit exceeded and high temperature David A Case
- Re: [AMBER] cyclic peptides and bond command in leap David A Case
- Re: [AMBER] cyclic peptides and bond command in leap Jonathan Gough
- Re: [AMBER] sqm Sofia Vasilakaki
- Re: [AMBER] cyclic peptides and bond command in leap Jonathan Gough
- Re: [AMBER] Antechamber error David A Case
- Re: [AMBER] cyclic peptides and bond command in leap David A Case
- Re: [AMBER] A question on binding free energy decomposition output wliu
- [AMBER] Fwd: Mail ceased to work in the last 72 hours George Tzotzos
- [AMBER] problem in plotting secondary structure graph Sehrish Naz
- [AMBER] Problems with the Amber-14 compilation and using MMPBSA.py with ubuntu ayesha kanwal
Wednesday, 16 September 2015
- Re: [AMBER] Simulation stops without errors Bala subramanian
- [AMBER] help in parallel run Robin Jain
- Re: [AMBER] query ankita mehta
- [AMBER] Test George Tzotzos
- Re: [AMBER] Problems with the Amber-14 compilation and using MMPBSA.py with ubuntu Jason Swails
- Re: [AMBER] Simulation stops without errors Jason Swails
- Re: [AMBER] help in parallel run Jason Swails
- Re: [AMBER] query Kenneth Huang
- Re: [AMBER] Problems with the Amber-14 compilation and using MMPBSA.py with ubuntu David A Case
- Re: [AMBER] Simulation stops without errors David A Case
- Re: [AMBER] help in parallel run David A Case
- Re: [AMBER] vlimit exceeded and high temperature Ruth Helena Tichauer
- Re: [AMBER] query David A Case
- Re: [AMBER] Contact map residues Daniel Roe
- [AMBER] cphmd reference energy Arjun Sharma
- Re: [AMBER] several peptides in my input can be identified by cpptraj? Daniel Roe
- Re: [AMBER] pca Daniel Roe
- Re: [AMBER] query ankita mehta
- Re: [AMBER] vlimit exceeded and high temperature Jason Swails
- Re: [AMBER] problem in plotting secondary structure graph Daniel Roe
- Re: [AMBER] cphmd reference energy Jason Swails
- Re: [AMBER] query Jason Swails
- Re: [AMBER] several peptides in my input can be identified by cpptraj? Fabian gmail
- Re: [AMBER] query ankita mehta
- [AMBER] Splitting LES trajectory Sergey Samsonov
- Re: [AMBER] query Nic Steussy
- Re: [AMBER] Splitting LES trajectory Daniel Roe
- [AMBER] DISAVE does not work on pmemd.cuda / GPU Mykola Dimura
- Re: [AMBER] query David A Case
- [AMBER] Michaelis complex Hector A. Baldoni
- [AMBER] Leap Connection of Covalent Unit Continued Robert Molt
- Re: [AMBER] Leap Connection of Covalent Unit Continued David A Case
- Re: [AMBER] DISAVE does not work on pmemd.cuda / GPU David A Case
Thursday, 17 September 2015
- Re: [AMBER] cyclic peptides and bond command in leap Anselm Horn
- Re: [AMBER] Simulation stops without errors Bala subramanian
- Re: [AMBER] Michaelis complex Jason Swails
- Re: [AMBER] Simulation stops without errors Jason Swails
- Re: [AMBER] Michaelis complex Hector A. Baldoni
- Re: [AMBER] Michaelis complex Carlos Simmerling
- [AMBER] antechamber error Atila Petrosian
- Re: [AMBER] antechamber error Atila Petrosian
- Re: [AMBER] Michaelis complex Jason Swails
- Re: [AMBER] Michaelis complex Jason Swails
- Re: [AMBER] antechamber error David A Case
- Re: [AMBER] Michaelis complex Carlos Simmerling
- Re: [AMBER] antechamber error Atila Petrosian
- Re: [AMBER] antechamber error hannes.loeffler.stfc.ac.uk
- Re: [AMBER] antechamber error Nic Steussy
- Re: [AMBER] Michaelis complex Hector A. Baldoni
- Re: [AMBER] Michaelis complex Jason Swails
- Re: [AMBER] Michaelis complex Carlos Simmerling
- Re: [AMBER] antechamber error David A Case
- Re: [AMBER] xmgrace in microsoft Martina Devi
- Re: [AMBER] xmgrace in microsoft Ye Mei
- Re: [AMBER] antechamber error Atila Petrosian
Friday, 18 September 2015
- [AMBER] Issues with gaff cd=cc atom type Francesco Pietra
- Re: [AMBER] vlimit exceeded and high temperature Ruth Helena Tichauer
- [AMBER] parmed.py Urszula Uciechowska
- Re: [AMBER] antechamber error Atila Petrosian
- Re: [AMBER] vlimit exceeded and high temperature Jason Swails
- Re: [AMBER] antechamber error Jason Swails
- Re: [AMBER] Issues with gaff cd=cc atom type Jason Swails
- Re: [AMBER] parmed.py Jason Swails
- Re: [AMBER] vlimit exceeded and high temperature Ruth Helena Tichauer
- Re: [AMBER] antechamber error David A Case
- Re: [AMBER] query ankita mehta
- [AMBER] MG ions being misplaced Kalenkiewicz, Andrew (NIH/NICHD) [F]
- [AMBER] Molecular Dynamics for Porphyrin Amber Maharaj
- Re: [AMBER] Molecular Dynamics for Porphyrin Jason Swails
- Re: [AMBER] Issues with gaff cd=cc atom type Francesco Pietra
- [AMBER] per residue decomposition MMPBSA Lara rajam
- Re: [AMBER] Issues with gaff cd=cc atom type Jason Swails
- Re: [AMBER] per residue decomposition MMPBSA Jason Swails
- Re: [AMBER] antechamber error Atila Petrosian
- Re: [AMBER] antechamber error Atila Petrosian
- Re: [AMBER] MG ions being misplaced David A Case
- Re: [AMBER] Molecular Dynamics for Porphyrin David A Case
- Re: [AMBER] antechamber error David A Case
- Re: [AMBER] antechamber error Atila Petrosian
- Re: [AMBER] Issues with gaff cd=cc atom type Francesco Pietra
- [AMBER] CpHMD for non protein residues Rahul Ramesh
- Re: [AMBER] CpHMD for non protein residues Jason Swails
- [AMBER] Minimization Marcelo Andrade Chagas
- Re: [AMBER] CpHMD for non protein residues Rahul Ramesh
- [AMBER] Calculating energy of solute Krantzman, Kristin D
- Re: [AMBER] Calculating energy of solute Christina Bergonzo
- Re: [AMBER] Issues with gaff cd=cc atom type Robert Molt
- [AMBER] Antechamber Flags Robert Molt
- Re: [AMBER] Antechamber Flags David A Case
Saturday, 19 September 2015
- Re: [AMBER] Issues with gaff cd=cc atom type Francesco Pietra
- [AMBER] ambertools14 Andrew Bostick
- Re: [AMBER] ambertools14 Jason Swails
- Re: [AMBER] Minimization Bill Ross
Sunday, 20 September 2015
- [AMBER] q4md FF with two "small" molecules Francesco Pietra
- [AMBER] on MD and Ramachandran outlier Brett
- Re: [AMBER] on MD and Ramachandran outlier Carlos Simmerling
- Re: [AMBER] q4md FF with two "small" molecules David A Case
- Re: [AMBER] q4md FF with two "small" molecules Francesco Pietra
- [AMBER] Extracting Information for each Frames Considered for Entropy Calculation by Normal Modes anilkumarsahoo.physics.iisc.ernet.in
- [AMBER] QM&Lipid14 Sofia Vasilakaki
- [AMBER] SHAKE&Vlimit 罗艳玲
- Re: [AMBER] Extracting Information for each Frames Considered for Entropy Calculation by Normal Modes Jason Swails
- [AMBER] Problem In Performing MMPBSA Calculation for System containing Ligand and Protein 杨川
Monday, 21 September 2015
- Re: [AMBER] QM&Lipid14 Ross Walker
- [AMBER] Fwd: q4md FF with two "small" molecules Francesco Pietra
- [AMBER] glycam parameter file Batuhan Kav
- Re: [AMBER] glycam parameter file Jason Swails
- Re: [AMBER] Problem In Performing MMPBSA Calculation for System containing Ligand and Protein Jason Swails
- Re: [AMBER] Fwd: q4md FF with two "small" molecules Jason Swails
- Re: [AMBER] SHAKE&Vlimit Jason Swails
- Re: [AMBER] SHAKE&Vlimit 罗艳玲
- Re: [AMBER] glycam parameter file Batuhan Kav
- Re: [AMBER] Extracting Information for each Frames Considered for Entropy Calculation by Normal Modes anilkumarsahoo.physics.iisc.ernet.in
- Re: [AMBER] glycam parameter file Jason Swails
- Re: [AMBER] glycam parameter file Lachele Foley
- [AMBER] warning when using cpptraj on BB atoms missing Fabian gmail
- Re: [AMBER] glycam parameter file Batuhan Kav
- Re: [AMBER] warning when using cpptraj on BB atoms missing Daniel Roe
- Re: [AMBER] SHAKE&Vlimit David A Case
- Re: [AMBER] warning when using cpptraj on BB atoms missing Fabian Glaser
- Re: [AMBER] Fwd: q4md FF with two "small" molecules Francesco Pietra
- [AMBER] Prospective research areas of AMBER Sabyasachi Sahoo
- Re: [AMBER] Prospective research areas of AMBER David A Case
- [AMBER] Freeze atoms to DM Marcelo Andrade Chagas
- Re: [AMBER] Freeze atoms to DM Gustavo Seabra
- Re: [AMBER] Freeze atoms to DM Jason Swails
- Re: [AMBER] Freeze atoms to DM Jason Swails
- Re: [AMBER] Freeze atoms to DM Marcelo Andrade Chagas
- [AMBER] Prepgen Robert Molt
- [AMBER] Problem In Performing MMPBSA Calculation for System containing Ligand and Protein 杨川
- [AMBER] Installing AMBER Wong Li Zhe
- [AMBER] distance based mask problem Chris
Tuesday, 22 September 2015
- [AMBER] Usage of off-diagonal coupling parameters for EVB model bijyalaxmi athokpam
- [AMBER] help in RDF Robin Jain
- Re: [AMBER] Prospective research areas of AMBER Sabyasachi Sahoo
- Re: [AMBER] Installing AMBER Hector A. Baldoni
- Re: [AMBER] Prepgen David A Case
- Re: [AMBER] distance based mask problem Jason Swails
- Re: [AMBER] Installing AMBER David A Case
- Re: [AMBER] help in RDF Jason Swails
- [AMBER] Protein - RNA modelling Sidhu, Khushwant (Dr.)
- [AMBER] degraded GPU performance Alessandro Contini (alessandro.contini)
- Re: [AMBER] help in RDF Tom Kurtzman
- Re: [AMBER] degraded GPU performance Ross Walker
- [AMBER] R: Re: degraded GPU performance Alessandro Contini
- Re: [AMBER] Problem In Performing MMPBSA Calculation for System containing Ligand and Protein Ray Luo, Ph.D.
- Re: [AMBER] Protein - RNA modelling Brian Radak
- [AMBER] Addions Na+ Marcelo Andrade Chagas
- Re: [AMBER] Addions Na+ Bill Ross
- Re: [AMBER] Addions Na+ Marcelo Andrade Chagas
- Re: [AMBER] Addions Na+ Kenneth Huang
- Re: [AMBER] Addions Na+ Jason Swails
- [AMBER] AMBER Tutorial B1 Backbone atoms Aishani Prem
- Re: [AMBER] Addions Na+ Bill Ross
- Re: [AMBER] AMBER Tutorial B1 Backbone atoms Thomas Cheatham
- Re: [AMBER] Addions Na+ Marcelo Andrade Chagas
- Re: [AMBER] Addions Na+ Jason Swails
- Re: [AMBER] Addions Na+ Marcelo Andrade Chagas
- [AMBER] Halogen bond force field in AMBER psu4.uic.edu
- Re: [AMBER] Halogen bond force field in AMBER Thomas Cheatham
- [AMBER] OpenMM Sofia Vasilakaki
- Re: [AMBER] OpenMM Hai Nguyen
- [AMBER] Implementation of GBSA in AMBER. Abhilash J
- Re: [AMBER] Implementation of GBSA in AMBER. Hai Nguyen
- Re: [AMBER] Implementation of GBSA in AMBER. Abhilash J
Wednesday, 23 September 2015
- [AMBER] Command for hbond analysis Martina Devi
- [AMBER] HELP in Emperical Valence bond model (EVB) bijyalaxmi athokpam
- Re: [AMBER] Halogen bond force field in AMBER Mahmoud A. A. Ibrahim
- [AMBER] Command for hbond analysis Daniel Roe
- Re: [AMBER] OpenMM Jason Swails
- Re: [AMBER] Implementation of GBSA in AMBER. Jason Swails
- Re: [AMBER] Addions Na+ David A Case
- Re: [AMBER] Command for hbond analysis Martina Devi
- [AMBER] Hoogsteen-Watson Base pair Martina Devi
- [AMBER] CpHMD simulation for non protein residues Rahul Ramesh
- Re: [AMBER] CpHMD simulation for non protein residues Jason Swails
- Re: [AMBER] CpHMD simulation for non protein residues Rahul Ramesh
- Re: [AMBER] HELP in Emperical Valence bond model (EVB) David A Case
- Re: [AMBER] Hoogsteen-Watson Base pair David A Case
- [AMBER] analysis from mixed amber 12 and amber 14 simulations George Green
- Re: [AMBER] Protein - RNA modelling David A Case
- Re: [AMBER] analysis from mixed amber 12 and amber 14 simulations David A Case
- Re: [AMBER] AMBER Tutorial B1 Backbone atoms Aishani Prem
- Re: [AMBER] analysis from mixed amber 12 and amber 14 simulations George Green
Thursday, 24 September 2015
- Re: [AMBER] hpc error Damiano Spadoni
- Re: [AMBER] hpc error Jason Swails
- Re: [AMBER] distance based mask problem Chris
- Re: [AMBER] hpc error David A Case
- Re: [AMBER] hpc error Jason Swails
- Re: [AMBER] distance based mask problem Daniel Roe
- Re: [AMBER] distance based mask problem Daniel Roe
- Re: [AMBER] HELP in Emperical Valence bond model (EVB) bijyalaxmi athokpam
- Re: [AMBER] hpc error Duke, Robert E Jr
- [AMBER] free -COOH at the C-terminus Xing
- Re: [AMBER] free -COOH at the C-terminus Jason Swails
- Re: [AMBER] free -COOH at the C-terminus Xing
- [AMBER] Membrane simulation without a membrane, only lipophilic solvent (membranemimetic) Marawan Hussien
- [AMBER] Membrane simulation without a membrane, only lipophilic solvent (membranemimetic) Marawan Hussien
- [AMBER] Membrane simulation without a membrane, only lipophilic solvent (membranemimetic) sridhar ganesan
Friday, 25 September 2015
- [AMBER] AMBER benchmarks Neha Gandhi
- Re: [AMBER] AMBER benchmarks Hannes Loeffler
- [AMBER] jfastw=4 and vlimit exceeded Ruth Helena Tichauer
- Re: [AMBER] jfastw=4 and vlimit exceeded Jason Swails
- [AMBER] adQMMM multiple solvation regions Covington, Cody Lance
- Re: [AMBER] jfastw=4 and vlimit exceeded Ruth Helena Tichauer
- Re: [AMBER] jfastw=4 and vlimit exceeded Jason Swails
- Re: [AMBER] jfastw=4 and vlimit exceeded Ruth Helena Tichauer
- [AMBER] T-REMD Reproducibility - Cluster v.s Desktop Thiago Lipinski Paes
- Re: [AMBER] T-REMD Reproducibility - Cluster v.s Desktop Carlos Simmerling
- Re: [AMBER] T-REMD Reproducibility - Cluster v.s Desktop Thiago Lipinski Paes
- Re: [AMBER] T-REMD Reproducibility - Cluster v.s Desktop Carlos Simmerling
- Re: [AMBER] T-REMD Reproducibility - Cluster v.s Desktop Jason Swails
- Re: [AMBER] T-REMD Reproducibility - Cluster v.s Desktop Gustavo Seabra
- [AMBER] Minimization of steps Marcelo Andrade Chagas
- Re: [AMBER] T-REMD Reproducibility - Cluster v.s Desktop Thiago Lipinski Paes
- Re: [AMBER] Minimization of steps David A Case
Saturday, 26 September 2015
- [AMBER] Fwd: ISC-2015-3BS-09 Sushi Shilpa
Sunday, 27 September 2015
- Re: [AMBER] hpc error Damiano Spadoni
- Re: [AMBER] hpc error Jason Swails
- Re: [AMBER] hpc error Duke, Robert E Jr
- [AMBER] wrap problem with QM/MM Covington, Cody Lance
- [AMBER] Problem with saving parameters for a complex having Heme group 杨川
Monday, 28 September 2015
- Re: [AMBER] wrap problem with QM/MM Marc van der Kamp
- Re: [AMBER] Problem with saving parameters for a complex having Heme group Jason Swails
- Re: [AMBER] Problem with saving parameters for a complex having Heme group David A Case
- Re: [AMBER] distance based mask problem Chris
- Re: [AMBER] wrap problem with QM/MM Covington, Cody Lance
- Re: [AMBER] distance based mask problem Daniel Roe
- Re: [AMBER] hpc error Jason Swails
- Re: [AMBER] clustering in PC subspace filip fratev
- Re: [AMBER] clustering in PC subspace filip fratev
- [AMBER] Updates for PBSA energy calculations Christina Berti
- Re: [AMBER] clustering in PC subspace filip fratev
- Re: [AMBER] clustering in PC subspace Daniel Roe
- Re: [AMBER] Updates for PBSA energy calculations Jason Swails
Tuesday, 29 September 2015
- [AMBER] 12 PhD positions for the Marie Skłodowska-Curie ITN-European MoGglyNet Alessandro Contini
- Re: [AMBER] Updates for PBSA energy calculations Ray Luo, Ph.D.
- [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal
- Re: [AMBER] Error: ptraj is needed for MMPBSA Daniel Roe
- [AMBER] Problem with saving parameters for a complex having Heme group 杨川
Wednesday, 30 September 2015
- [AMBER] Amber compilation problem Weinzierl, Robert O J
- Re: [AMBER] Amber compilation problem Theoretical Research
- Re: [AMBER] Amber compilation problem Jason Swails
- [AMBER] Need help regarding references Saikat Dutta chowdhury
- Re: [AMBER] Need help regarding references Carlos Simmerling
- Re: [AMBER] Need help regarding references Saikat Dutta chowdhury
- Re: [AMBER] Need help regarding references Carlos Simmerling
- Re: [AMBER] Need help regarding references Gustavo Seabra
- Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal
- Re: [AMBER] Error: ptraj is needed for MMPBSA Jason Swails
- Re: [AMBER] Updates for PBSA energy calculations Christina Berti
- [AMBER] Oxygen parameters for AMBER99SB-ILDN Ebert Maximilian
- Re: [AMBER] Oxygen parameters for AMBER99SB-ILDN Jason Swails
- Re: [AMBER] Oxygen parameters for AMBER99SB-ILDN Ebert Maximilian
- Re: [AMBER] Updates for PBSA energy calculations David A Case
- Re: [AMBER] Updates for PBSA energy calculations Christina Berti
- Re: [AMBER] Updates for PBSA energy calculations Jason Swails

Last message date: Wed Sep 30 2015 - 15:30:03 PDT
Archived on: Fri Nov 15 2024 - 05:55:17 PST

Amber Archive Sep 2015 by date