Amber Archive Jul 2014: by date

Monday, 30 June 2014
- [AMBER] AmberTools parallel test experienced errors sunita.tifrh.res.in
Tuesday, 1 July 2014
- [AMBER] RDF zahra khatti
- Re: [AMBER] Setting up z-constraint Pierpaolo Cacciotto
- Re: [AMBER] AmberTools parallel test experienced errors David A Case
- [AMBER] support of "center of mass restraint" Takeshi Baba
- Re: [AMBER] support of "center of mass restraint" Jason Swails
- [AMBER] sander error "Could not find cntrl namelist" Asmita Gupta
- Re: [AMBER] sander error "Could not find cntrl namelist" Jason Swails
- Re: [AMBER] RDF Brian Radak
- [AMBER] Cuda tests failure on GeForce GTX 780 Serzhan Sakipov
- Re: [AMBER] sander error "Could not find cntrl namelist" Asmita Gupta
- Re: [AMBER] cpptraj: arithmetic on data sets? Daniel Roe
- [AMBER] about setting nscm kirtana S
- Re: [AMBER] Cuda tests failure on GeForce GTX 780 Jason Swails
- Re: [AMBER] sander error "Could not find cntrl namelist" David A Case
- Re: [AMBER] periodic box drifted during NVE run Quynh Vo
- [AMBER] ZAFF-CCCH Histidine charge problem Christy Lee
- Re: [AMBER] ZAFF-CCCH Histidine charge problem Pengfei Li
- Re: [AMBER] about setting nscm Jason Swails
- [AMBER] Visualizing average solvent-oxygen density/occupancy from an MD trajectory Abhishek Mukhopadhyay
- [AMBER] Understand the AMBER coordinate files Wujie Wang
- [AMBER] grid analysis Mary Varughese
- Re: [AMBER] Understand the AMBER coordinate files Ross Walker
Wednesday, 2 July 2014
- [AMBER] Fwd: error: unable to generate parameter file Harmeet Kaur
- Re: [AMBER] Fwd: error: unable to generate parameter file Soumendranath Bhakat
- [AMBER] Extracting total energy and other enegy componenets of ligand Soumendranath Bhakat
- [AMBER] How to Extract Energy Contribution of Ligand Only Soumendranath Bhakat
- [AMBER] MM-PBSA Zeinab Tavasoli
- [AMBER] No parameters for PGR in lipid14 Niels Geudens
- Re: [AMBER] No parameters for PGR in lipid14 Dickson, Callum J
- Re: [AMBER] periodic box drifted during NVE run David A Case
- Re: [AMBER] MM-PBSA David A Case
- Re: [AMBER] MM-PBSA Soumendranath Bhakat
- Re: [AMBER] No parameters for PGR in lipid14 Niels Geudens
- [AMBER] NMR distance restrains Valentina Romano
- Re: [AMBER] Understand the AMBER coordinate files Wujie Wang
- Re: [AMBER] Visualizing average solvent-oxygen density/occupancy from an MD trajectory Daniel Roe
- Re: [AMBER] No parameters for PGR in lipid14 Jason Swails
- Re: [AMBER] grid analysis Daniel Roe
- Re: [AMBER] MM-PBSA Jason Swails
- Re: [AMBER] NMR distance restrains David A Case
- Re: [AMBER] sander error "Could not find cntrl namelist" Asmita Gupta
- Re: [AMBER] Extracting total energy and other enegy componenets of ligand Daniel Roe
- Re: [AMBER] Understand the AMBER coordinate files Daniel Roe
- Re: [AMBER] QM on Adenosine Steven M. Graham
- Re: [AMBER] MM-PBSA Soumendranath Bhakat
- Re: [AMBER] NMR distance restrains Valentina Romano
- Re: [AMBER] QM on Adenosine Christina Bergonzo
- Re: [AMBER] NMR distance restrains David A Case
- [AMBER] Attempting to compile fresh version of Amber 11, bugfixes > 17 won't apply cleanly Bob Healey
- Re: [AMBER] support of "center of mass restraint" Takeshi Baba
- Re: [AMBER] support of "center of mass restraint" Ross Walker
- Re: [AMBER] MM-PBSA Jason Swails
- Re: [AMBER] support of "center of mass restraint" Takeshi Baba
- Re: [AMBER] Attempting to compile fresh version of Amber 11, bugfixes > 17 won't apply cleanly Jason Swails
- Re: [AMBER] support of "center of mass restraint" Gustavo Seabra
- Re: [AMBER] grid analysis Mary Varughese
- [AMBER] high energy output kirtana S
- Re: [AMBER] high energy output Ross Walker
- Re: [AMBER] grid analysis Daniel Roe
- [AMBER] Issues Compiling AmberTools13 Malachi Phillips
- Re: [AMBER] Issues Compiling AmberTools13 Jason Swails
- Re: [AMBER] ZAFF-CCCH Histidine charge problem Christy Lee
- Re: [AMBER] ZAFF-CCCH Histidine charge problem Pengfei Li
- Re: [AMBER] grid analysis Mary Varughese
Thursday, 3 July 2014
- Re: [AMBER] NMR distance restrains Valentina Romano
- [AMBER] Debug amber energy parameters Ramuntcho Moretti
- [AMBER] Wrong number of restrained atoms Valentina Romano
- [AMBER] Failed to generate parameter file Vishal Nemaysh
- Re: [AMBER] Failed to generate parameter file Soumendranath Bhakat
- Re: [AMBER] Failed to generate parameter file David A Case
- Re: [AMBER] Wrong number of restrained atoms David A Case
- [AMBER] ncsu_smd support in pmemd amber12 Asmita Gupta
- [AMBER] neighbours around an atom Krisztina Feher
- Re: [AMBER] ncsu_smd support in pmemd amber12 Jason Swails
- Re: [AMBER] Debug amber energy parameters Daniel Roe
- [AMBER] Time information lost. Domenico Marson
- Re: [AMBER] neighbours around an atom Jason Swails
- Re: [AMBER] neighbours around an atom Daniel Roe
- Re: [AMBER] Time information lost. Daniel Roe
- [AMBER] amoeba into ambertools Jorgen Simonsen
- [AMBER] PMEMD running on Intel Xeon Phi Hai Long
- Re: [AMBER] Visualizing average solvent-oxygen density/occupancy from an MD trajectory Eric Pettersen
- [AMBER] MMPBSA Energy between system and its image Ahmed Ayoub
- Re: [AMBER] amoeba into ambertools Jason Swails
- Re: [AMBER] MMPBSA Energy between system and its image Jason Swails
- Re: [AMBER] periodic box drifted during NVE run Quynh Vo
- Re: [AMBER] ZAFF-CCCH Histidine charge problem Christy Lee
- [AMBER] How to strip water from .mdcrd file? Wujie Wang
- Re: [AMBER] PMEMD running on Intel Xeon Phi Scott Le Grand
- Re: [AMBER] PMEMD running on Intel Xeon Phi Ross Walker
Friday, 4 July 2014
- Re: [AMBER] How to strip water from .mdcrd file? Soumendranath Bhakat
- [AMBER] errors in compiling AmberTools14 Alessandro Contini
- [AMBER] MMPBSA Sourav Purohit
- [AMBER] Fwd: neighbours around an atom Krisztina Fehér
- [AMBER] Fwd: neighbours around an atom Krisztina Fehér
- Re: [AMBER] Fwd: neighbours around an atom Krisztina Feher
- [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Mele N.
- Re: [AMBER] How to strip water from .mdcrd file? Wujie Wang
- Re: [AMBER] How to strip water from .mdcrd file? Wujie Wang
- Re: [AMBER] Fwd: neighbours around an atom Daniel Roe
- Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Daniel Roe
- Re: [AMBER] MMPBSA Jason Swails
- Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Mele N.
- Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Jason Swails
- Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Mele N.
- Re: [AMBER] MMPBSA Energy between system and its image Ahmed Ayoub
- Re: [AMBER] MMPBSA Energy between system and its image Jason Swails
Saturday, 5 July 2014
- Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Mele N.
- Re: [AMBER] Fwd: neighbours around an atom Krisztina Fehér
- Re: [AMBER] Fwd: neighbours around an atom Jason Swails
- Re: [AMBER] Fwd: neighbours around an atom Daniel Roe
- Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Daniel Roe
- Re: [AMBER] Fwd: neighbours around an atom Krisztina Fehér
- Re: [AMBER] Fwd: neighbours around an atom Krisztina Fehér
Sunday, 6 July 2014
- Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Mele N.
- Re: [AMBER] ZAFF-CCCH Histidine charge problem Pengfei Li
- [AMBER] imaging problem Jonathan Gough
Monday, 7 July 2014
- [AMBER] Build Xleap Baptiste Legrand
- [AMBER] errors in compiling AmberTools14 Alessandro Contini
- [AMBER] Imaging issue Michael Criddle
- [AMBER] questions on output files of hbond analysis zhangmk
- Re: [AMBER] Build Xleap David A Case
- Re: [AMBER] Imaging issue David A Case
- Re: [AMBER] Build Xleap Baptiste Legrand
- Re: [AMBER] questions on output files of hbond analysis Daniel Roe
- Re: [AMBER] imaging problem Daniel Roe
- Re: [AMBER] Build Xleap David A Case
- Re: [AMBER] errors in compiling AmberTools14 Jason Swails
- Re: [AMBER] errors in compiling AmberTools14 Alessandro Contini
- Re: [AMBER] Build Xleap Baptiste Legrand
- Re: [AMBER] PMEMD running on Intel Xeon Phi Hai Long
- Re: [AMBER] ZAFF-CCCH Histidine charge problem Christy Lee
- Re: [AMBER] ZAFF-CCCH Histidine charge problem Pengfei Li
- [AMBER] inositol hexakisphosphate Hector A. Baldoni
- Re: [AMBER] ZAFF-CCCH Histidine charge problem Christy Lee
- Re: [AMBER] questions on output files of hbond analysis zhangmk
- [AMBER] cpptraj hbond Neha Gandhi
Tuesday, 8 July 2014
- [AMBER] ATP and Mg2+ parameters Valentina Romano
- Re: [AMBER] ATP and Mg2+ parameters Soumendranath Bhakat
- Re: [AMBER] ATP and Mg2+ parameters Hector A. Baldoni
- Re: [AMBER] ATP and Mg2+ parameters Alessandro Contini
- Re: [AMBER] questions on output files of hbond analysis David A Case
- [AMBER] RESP fitting with group restraint Niels Geudens
- [AMBER] imin=5, maxcyc>1 stalls Allen, Scott Edward
- [AMBER] Problem with MMPBSA.py Rajeswari A.
- Re: [AMBER] imaging problem Jonathan Gough
- Re: [AMBER] ATP and Mg2+ parameters Valentina Romano
- Re: [AMBER] ZAFF-CCCH Histidine charge problem Pengfei Li
- Re: [AMBER] inositol hexakisphosphate FyD
- Re: [AMBER] ATP and Mg2+ parameters FyD
- Re: [AMBER] imin=5, maxcyc>1 stalls Jason Swails
- [AMBER] R: Re: ATP and Mg2+ parameters Alessandro Contini
- Re: [AMBER] RESP fitting with group restraint FyD
- Re: [AMBER] ATP and Mg2+ parameters Jason Swails
- Re: [AMBER] Problem with MMPBSA.py Jason Swails
- Re: [AMBER] imin=5, maxcyc>1 stalls Allen, Scott Edward
- [AMBER] Issues running RED ESP software Malachi Phillips
- [AMBER] pmemdTI test failure Blake Mertz
- Re: [AMBER] imaging problem Daniel Roe
- [AMBER] Parameter file for polyethyleglycol PEG Iqbal, Muhammad Sajid
Monday, 7 July 2014
- Re: [AMBER] RESP fitting with group restraint niels.geudens.ugent.be
Tuesday, 8 July 2014
- Re: [AMBER] Parameter file for polyethyleglycol PEG Jason Swails
- Re: [AMBER] imaging problem Jonathan Gough
- Re: [AMBER] pmemdTI test failure David A Case
- Re: [AMBER] imaging problem Daniel Roe
- Re: [AMBER] cpptraj hbond Daniel Roe
- [AMBER] atomiccorr: glibc detected *** cpptraj: malloc(): memory corruption: Krisztina Feher
- [AMBER] Orbital Hessian Not Positive Definite Error Malachi Phillips
- Re: [AMBER] atomiccorr: glibc detected *** cpptraj: malloc(): memory corruption: Jason Swails
- Re: [AMBER] atomiccorr: glibc detected *** cpptraj: malloc(): memory corruption: Jason Swails
- [AMBER] how to quantify and visualize the flow of water into a protein Thomas Evangelidis
- Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Daniel Roe
- Re: [AMBER] atomiccorr: glibc detected *** cpptraj: malloc(): memory corruption: Daniel Roe
- Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Jason Swails
- [AMBER] entropy Calculation Him Shweta
- Re: [AMBER] Problem with MMPBSA.py Rajeswari A.
- Re: [AMBER] entropy Calculation Jason Swails
- Re: [AMBER] Problem with MMPBSA.py Jason Swails
Wednesday, 9 July 2014
- Re: [AMBER] Loop refirement James Starlight
- Re: [AMBER] cpptraj hbond Neha Gandhi
- [AMBER] Question Brittany Boykin
- Re: [AMBER] Question Daniel Roe
- [AMBER] Finding a good REMD temperature ladder Eugene Yedvabny
- [AMBER] autoimage doesn't work 肖立
- Re: [AMBER] autoimage doesn't work Daniel Roe
- Re: [AMBER] autoimage doesn't work 肖立
- Re: [AMBER] autoimage doesn't work 肖立
- Re: [AMBER] Finding a good REMD temperature ladder Daniel Roe
- Re: [AMBER] Finding a good REMD temperature ladder Carlos Simmerling
- [AMBER] tinker to amber format Jorgen Simonsen
Thursday, 10 July 2014
- [AMBER] Switch function in Amber Ramuntcho Moretti
- [AMBER] Ag+ ion parameters Rebeca García Fandiño
- [AMBER] DCCP analysis Soumendranath Bhakat
- [AMBER] Fwd: Re: [q4md-fft] Issues Running, missing Ante_RED 2 FyD
- Re: [AMBER] Loop refirement James Starlight
- Re: [AMBER] Parameter file for polyethyleglycol PEG FyD
- [AMBER] Fwd: Re: [q4md-fft] URGENT:Orbital Hessian Not Positive Definite FyD
- Re: [AMBER] tinker to amber format Jason Swails
- Re: [AMBER] Switch function in Amber David A Case
- Re: [AMBER] entropy Calculation Him Shweta
- [AMBER] Free Binding Energy Calculation Him Shweta
- Re: [AMBER] Free Binding Energy Calculation Bill Miller III
- Re: [AMBER] Free Binding Energy Calculation Him Shweta
- Re: [AMBER] DCCP analysis Daniel Roe
- Re: [AMBER] entropy Calculation Him Shweta
- [AMBER] Sander of Amber11, Amber12 and AmberTools14 Massimiliano Porrini
- Re: [AMBER] entropy Calculation Jason Swails
- Re: [AMBER] Sander of Amber11, Amber12 and AmberTools14 Jason Swails
- Re: [AMBER] ZAFF-CCCH Histidine charge problem Christy Lee
- [AMBER] cpptraj rotdif parameters Alegrete, Matthew
- [AMBER] How is temperature in Amber MD simulations calculated? Arthur Roberts
- Re: [AMBER] How is temperature in Amber MD simulations calculated? Brian Radak
- Re: [AMBER] How is temperature in Amber MD simulations calculated? Jason Swails
- [AMBER] Question Brittany Boykin
- Re: [AMBER] Question Jason Swails
- Re: [AMBER] ZAFF-CCCH Histidine charge problem Pengfei Li
- Re: [AMBER] ZAFF-CCCH Histidine charge problem Yue
- Re: [AMBER] cpptraj rotdif parameters David A Case
- Re: [AMBER] entropy Calculation Him Shweta
- [AMBER] evaluating hydrogen bond using ptraj Vijay Manickam Achari
Friday, 11 July 2014
- [AMBER] cholesterol with lipid14 Thomas Evangelidis
- Re: [AMBER] parmchk2 segfaults Sushil Mishra
- [AMBER] Thermodynamic Integration by using pmemd Sun
- Re: [AMBER] Thermodynamic Integration by using pmemd Hannes Loeffler
- Re: [AMBER] Sander of Amber11, Amber12 and AmberTools14 Massimiliano Porrini
- Re: [AMBER] Thermodynamic Integration by using pmemd Ying-Chieh Sun
- Re: [AMBER] Ag+ ion parameters Pengfei Li
- Re: [AMBER] parmchk2 segfaults Jason Swails
- [AMBER] graph energy check after minimization amor san juan
- [AMBER] diffusion path length newamber list
- Re: [AMBER] graph energy check after minimization Jason Swails
- Re: [AMBER] diffusion path length Daniel Roe
- Re: [AMBER] diffusion path length newamber list
- [AMBER] cuda.test errors Jonathan Gough
- Re: [AMBER] cuda.test errors Ross Walker
Saturday, 12 July 2014
- Re: [AMBER] graph energy check after minimization amor san juan
- Re: [AMBER] cuda.test errors Jonathan Gough
- Re: [AMBER] diffusion path length newamber list
- [AMBER] pressure tensor kirtana S
- Re: [AMBER] diffusion path length Daniel Roe
- Re: [AMBER] diffusion path length newamber list
Sunday, 13 July 2014
- [AMBER] Query about QM/MM scanning using amber Kshatresh Dutta Dubey
- Re: [AMBER] Query about QM/MM scanning using amber Jason Swails
Monday, 14 July 2014
- [AMBER] hydrogen bond evaluation Vijay Manickam Achari
- [AMBER] cpptraj help Saikat Dutta chowdhury
- Re: [AMBER] cpptraj help Daniel Roe
- Re: [AMBER] cpptraj help Saikat Dutta chowdhury
- Re: [AMBER] hydrogen bond evaluation Jason Swails
- Re: [AMBER] diffusion path length Daniel Roe
- Re: [AMBER] hydrogen bond evaluation Daniel Roe
- Re: [AMBER] diffusion path length newamber list
- [AMBER] update amber12 zahra khatti
- [AMBER] coordinate and topology files using tleap from RED server output files Iqbal, Muhammad Sajid
- Re: [AMBER] update amber12 Jason Swails
- [AMBER] Downloading old versions of AMBERTools Marawan Hussien
- Re: [AMBER] Downloading old versions of AMBERTools Jason Swails
Tuesday, 15 July 2014
- [AMBER] gpu and cpu runs Mary Varughese
- [AMBER] Error output file Faez Iqbal khan
- Re: [AMBER] Error output file Soumendranath Bhakat
- Re: [AMBER] Error output file Soumendranath Bhakat
- [AMBER] Error while running tleap Suchetana Gupta
- Re: [AMBER] ATP and Mg2+ parameters Valentina Romano
- Re: [AMBER] coordinate and topology files using tleap from RED server output files FyD
- Re: [AMBER] ATP and Mg2+ parameters FyD
- [AMBER] nativecontacts by amber14 cpptraj Rajeswari A.
- [AMBER] Could not find cntrl namelist Fengxue Li
- Re: [AMBER] Could not find cntrl namelist Pengfei Li
- [AMBER] To get resp charges of a modified central residue (not an integer). Baptiste Legrand
- Re: [AMBER] hydrogen bond evaluation Jason Swails
- Re: [AMBER] gpu and cpu runs Jason Swails
- Re: [AMBER] Error output file Jason Swails
- Re: [AMBER] Error while running tleap Jason Swails
- Re: [AMBER] Error while running tleap Suchetana Gupta
- Re: [AMBER] To get resp charges of a modified central residue (not an integer). Jason Swails
- Re: [AMBER] Downloading old versions of AMBERTools Marawan Hussien
- Re: [AMBER] nativecontacts by amber14 cpptraj Daniel Roe
- Re: [AMBER] Downloading old versions of AMBERTools Jason Swails
- Re: [AMBER] pressure tensor Jason Swails
- Re: [AMBER] gpu and cpu runs Mary Varughese
- Re: [AMBER] gpu and cpu runs Jason Swails
- Re: [AMBER] gpu and cpu runs Mary Varughese
- Re: [AMBER] nativecontacts by amber14 cpptraj Rajeswari A.
- Re: [AMBER] To get resp charges of a modified central residue (not an integer). FyD
Wednesday, 16 July 2014
- [AMBER] installation of AMBER 12 in MAC 10.7 lion Vishal Nemaysh
- [AMBER] RNA covalent bond angles Blatter Markus
- Re: [AMBER] problem in "re-image" and "unwarp" Him Shweta
- [AMBER] Tool in PTRAJ/CPPTRAJ to analyse residue movement anu chandra
- Re: [AMBER] Tool in PTRAJ/CPPTRAJ to analyse residue movement Soumendranath Bhakat
- Re: [AMBER] installation of AMBER 12 in MAC 10.7 lion David A Case
- [AMBER] Problem with atommap in cpptraj Rajeswari A.
- Re: [AMBER] RNA covalent bond angles Christina Bergonzo
- Re: [AMBER] RNA covalent bond angles Blatter Markus
- Re: [AMBER] RNA covalent bond angles Niel Henriksen
- Re: [AMBER] Loop refirement Carlos Simmerling
- Re: [AMBER] RNA covalent bond angles Blatter Markus
- [AMBER] ATP parameters: tleap error Valentina Romano
- Re: [AMBER] ATP parameters: tleap error Jason Swails
- Re: [AMBER] gpu and cpu runs Ross Walker
- Re: [AMBER] gpu and cpu runs Scott Le Grand
- [AMBER] How do I apply cpptraj.timecorr to the output dataset of cpptraj.dihedral? Jose Borreguero
- Re: [AMBER] gpu and cpu runs Mary Varughese
- Re: [AMBER] Problem with atommap in cpptraj Daniel Roe
- Re: [AMBER] How do I apply cpptraj.timecorr to the output dataset of cpptraj.dihedral? Daniel Roe
- Re: [AMBER] ATP parameters: tleap error George Patargias
Thursday, 17 July 2014
- [AMBER] Implicit solvent and membrane protein James Starlight
- Re: [AMBER] Loop refirement James Starlight
- Re: [AMBER] To get resp charges of a modified central residue (not an integer). Baptiste Legrand
- Re: [AMBER] Loop refirement James Starlight
- Re: [AMBER] Loop refirement Carlos Simmerling
- [AMBER] Error installing Ambertools on Centos 6.3 and open suse 12.3 Charu Suri
- Re: [AMBER] How do I apply cpptraj.timecorr to the output dataset of cpptraj.dihedral? Jose Borreguero
- Re: [AMBER] Error installing Ambertools on Centos 6.3 and open suse 12.3 Jason Swails
- [AMBER] imin=5 Lara rajam
- Re: [AMBER] imin=5 Carlos Simmerling
- Re: [AMBER] imin=5 Brian Radak
- Re: [AMBER] Loop refirement James Starlight
- Re: [AMBER] To get resp charges of a modified central residue (not an integer). FyD
- Re: [AMBER] imin=5 Lara rajam
- Re: [AMBER] Loop refirement James Starlight
- [AMBER] iwrap Sourav Purohit
- Re: [AMBER] Loop refirement Carlos Simmerling
- Re: [AMBER] Loop refirement Carlos Simmerling
- Re: [AMBER] Loop refirement James Starlight
- Re: [AMBER] iwrap Teerapong Pirojsirikul
- Re: [AMBER] Implicit solvent and membrane protein Ray Luo, Ph.D.
- Re: [AMBER] How do I apply cpptraj.timecorr to the output dataset of cpptraj.dihedral? Jose Borreguero
- Re: [AMBER] Implicit solvent and membrane protein James Starlight
- Re: [AMBER] Implicit solvent and membrane protein Carlos Simmerling
- [AMBER] parameterizing a connected moiety Mohammad Salem
- Re: [AMBER] parameterizing a connected moiety Jason Swails
- [AMBER] ScaledMD for proline dipeptide Niels Geudens
- Re: [AMBER] ScaledMD for proline dipeptide Jason Swails
Friday, 18 July 2014
- Re: [AMBER] ScaledMD for proline dipeptide Niels Geudens
- Re: [AMBER] ScaledMD for proline dipeptide Jason Swails
- Re: [AMBER] Implicit solvent and membrane protein James Starlight
- Re: [AMBER] Implicit solvent and membrane protein Thomas Evangelidis
- Re: [AMBER] Implicit solvent and membrane protein James Starlight
- Re: [AMBER] Implicit solvent and membrane protein Thomas Evangelidis
- Re: [AMBER] Implicit solvent and membrane protein James Starlight
- [AMBER] Fwd: problem in installation of ambertools14 Vidushi Sharma
- Re: [AMBER] Fwd: problem in installation of ambertools14 Raman Parkesh
- Re: [AMBER] Fwd: problem in installation of ambertools14 David A Case
- Re: [AMBER] parameterizing a connected moiety FyD
- [AMBER] Electrostatic energy calculated by MD in MM/GBSA menwer momo
- Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA Jason Swails
- Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA menwer momo
- Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA Jason Swails
- Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA Jason Swails
- Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA Jason Swails
- Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA menwer momo
Saturday, 19 July 2014
- [AMBER] memory allocation error for *bond Vishal Nemaysh
- [AMBER] Hydrogen bond analysis menwer momo
- [AMBER] mailing list problem Vidushi Sharma
- Re: [AMBER] Fwd: problem in installation of ambertools14 Hirdesh Kumar
- Re: [AMBER] memory allocation error for *bond David A Case
- Re: [AMBER] Fwd: problem in installation of ambertools14 David A Case
- [AMBER] X11 error Vidushi Sharma
- Re: [AMBER] X11 error David A Case
- Re: [AMBER] memory allocation error for *bond Vishal Nemaysh
Sunday, 20 July 2014
- [AMBER] memory allocation error for *bond Vishal Nemaysh
- Re: [AMBER] memory allocation error for *bond David A Case
- [AMBER] Lipid and protein - error reading group during heat Jonathan Gough
Monday, 21 July 2014
- [AMBER] NVT and NPT ensemble Sangita Kachhap
- Re: [AMBER] NVT and NPT ensemble Soumendranath Bhakat
- [AMBER] Amber12 CUDA problems Lorenzo Gontrani
- Re: [AMBER] Lipid and protein - error reading group during heat David A Case
- Re: [AMBER] bash scripting for MD tasks James Starlight
- Re: [AMBER] Amber12 CUDA problems Ross Walker
- Re: [AMBER] bash scripting for MD tasks Parker de Waal
- [AMBER] error in md simulation in pmemd.cuda.MPI Subrata Paul
- [AMBER] Fwd: error in md simulation in pmemd.cuda.MPI Subrata Paul
- Re: [AMBER] Amber12 CUDA problems Lorenzo Gontrani
- Re: [AMBER] Amber12 CUDA problems Lorenzo Gontrani
- Re: [AMBER] error in md simulation in pmemd.cuda.MPI Ross Walker
Tuesday, 22 July 2014
- [AMBER] Regarding LIE in cpptraj Kshatresh Dutta Dubey
- [AMBER] AMP Parameters cye927.mail.ustc.edu.cn
- Re: [AMBER] Regarding LIE in cpptraj Daniel Roe
- Re: [AMBER] Hydrogen bond analysis Daniel Roe
- [AMBER] sander.APBS: automatic grid adjustments in output? Brian Radak
- [AMBER] Unable to compile cuda version of amber14 Manikanthan Bhavaraju
- Re: [AMBER] Unable to compile cuda version of amber14 Jason Swails
- [AMBER] help Zeynep Topdemir
- Re: [AMBER] help Jason Swails
- Re: [AMBER] help David A Case
- [AMBER] atom number same as line number for cpptraj newamber list
- Re: [AMBER] atom number same as line number for cpptraj Jason Swails
- Re: [AMBER] atom number same as line number for cpptraj Daniel Roe
- [AMBER] Hello SaeeD PourasaD
- Re: [AMBER] NVT and NPT ensemble Raman Parkesh
- Re: [AMBER] Hello Pengfei Li
- Re: [AMBER] sander.APBS: automatic grid adjustments in output? Robert Konecny
- Re: [AMBER] NVT and NPT ensemble Sangita Kachhap
- [AMBER] GIST - unusually high water-water energies Waldner, Birgit
Wednesday, 23 July 2014
- Re: [AMBER] AMP Parameters FyD
- [AMBER] On the values of boost potential for aMD based on amd.log James Starlight
- [AMBER] Z-axis coordinates Him Shweta
- Re: [AMBER] Hello David A Case
- Re: [AMBER] sander.APBS: automatic grid adjustments in output? Brian Radak
- Re: [AMBER] Z-axis coordinates Daniel Roe
- Re: [AMBER] On the values of boost potential for aMD based on amd.log Daniel Roe
- Re: [AMBER] Z-axis coordinates Him Shweta
- Re: [AMBER] On the values of boost potential for aMD based on amd.log James Starlight
- Re: [AMBER] atom number same as line number for cpptraj newamber list
- Re: [AMBER] On the values of boost potential for aMD based on amd.log Thomas Evangelidis
- Re: [AMBER] On the values of boost potential for aMD based on amd.log Brian Radak
- Re: [AMBER] atom number same as line number for cpptraj Jason Swails
- Re: [AMBER] atom number same as line number for cpptraj newamber list
- [AMBER] Bug in tleap savemol2? David Minh
- Re: [AMBER] Bug in tleap savemol2? Jason Swails
- Re: [AMBER] On the values of boost potential for aMD based on amd.log James Starlight
- Re: [AMBER] Bug in tleap savemol2? David Minh
- [AMBER] ptraj binary missing from AmberTools 13 install? Raik Grünberg
- Re: [AMBER] ptraj binary missing from AmberTools 13 install? Raik Grünberg
- Re: [AMBER] ptraj binary missing from AmberTools 13 install? Daniel Roe
- [AMBER] renumber all residues in prmtop Thomas Evangelidis
- Re: [AMBER] ptraj binary missing from AmberTools 13 install? Raik Grünberg
- Re: [AMBER] ptraj binary missing from AmberTools 13 install? Jason Swails
- Re: [AMBER] renumber all residues in prmtop Jason Swails
Thursday, 24 July 2014
- Re: [AMBER] renumber all residues in prmtop Thomas Evangelidis
- [AMBER] Hi SaeeD PourasaD
- Re: [AMBER] Hi Marc van der Kamp
- Re: [AMBER] renumber all residues in prmtop David A Case
- [AMBER] CYM charges in amino14ipq.lib wrong? Marc van der Kamp
- Re: [AMBER] CYM charges in amino14ipq.lib wrong? David A Case
- Re: [AMBER] GPU error Attempting MC barostat change: Failed Raman Parkesh
- Re: [AMBER] parmchk2 segfaults Hannes Loeffler
- [AMBER] Cpptraj clustering James Starlight
- [AMBER] pbc problem Niloofar Nayebi
- [AMBER] Not integer charge for glycoprotein Tommaso Casalini
- Re: [AMBER] Not integer charge for glycoprotein Lachele Foley
- Re: [AMBER] GPU error Attempting MC barostat change: Failed Jason Swails
- Re: [AMBER] pbc problem David A Case
- Re: [AMBER] parmchk2 segfaults Jason Swails
- [AMBER] cpptraj not processing all mdcrd files Kshatresh Dutta Dubey
- [AMBER] problems with paramfit Marek Maly
- Re: [AMBER] GPU error Attempting MC barostat change: Failed Raman Parkesh
- [AMBER] Berendsen vs. Monte Carlo Parker de Waal
- [AMBER] values of λ in Thermodynamic Integration Sun
- Re: [AMBER] values of λ in Thermodynamic Integration Ying-Chieh Sun
- Re: [AMBER] GPU error Attempting MC barostat change: Failed Jason Swails
- Re: [AMBER] Berendsen vs. Monte Carlo Jason Swails
Friday, 25 July 2014
- [AMBER] element symbol error in tleap cq y
- [AMBER] element symbol error in tleap Changqing Yan
- Re: [AMBER] element symbol error in tleap Changqing Yan
- [AMBER] Hi Him Shweta
- Re: [AMBER] parmchk2 segfaults Hannes Loeffler
- Re: [AMBER] values of λ in Thermodynamic Integration David A Case
- Re: [AMBER] element symbol error in tleap David A Case
- Re: [AMBER] Berendsen vs. Monte Carlo Parker de Waal
- Re: [AMBER] Berendsen vs. Monte Carlo Brian Radak
- Re: [AMBER] problems with paramfit Robin Betz
- Re: [AMBER] problems with paramfit Marek Maly
- Re: [AMBER] cpptraj not processing all mdcrd files Daniel Roe
- [AMBER] Running PCA Nicole Ippolito
- [AMBER] Fwd: AMBER Digest, Vol 926, Issue 1 Changqing Yan
Saturday, 26 July 2014
- [AMBER] On the ussage of the langevens thermostat with the gb models James Starlight
- Re: [AMBER] On the ussage of the langevens thermostat with the gb models Carlos Simmerling
- Re: [AMBER] Fwd: AMBER Digest, Vol 926, Issue 1 David A Case
Sunday, 27 July 2014
- Re: [AMBER] problems with paramfit Marek Maly
- [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process Marek Maly
- [AMBER] Problem on making inpcrd file 肖立
- Re: [AMBER] Problem on making inpcrd file David A Case
Monday, 28 July 2014
- Re: [AMBER] On the ussage of the langevens thermostat with the gb models James Starlight
- Re: [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process Marc van der Kamp
- Re: [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process David A Case
- [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas
- Re: [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process Marek Maly
- [AMBER] PMF by WHAM Marta Wisniewska
- Re: [AMBER] Problem on making inpcrd file Jason Swails
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Jason Swails
- Re: [AMBER] PMF by WHAM Brian Radak
- Re: [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process Jason Swails
- Re: [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process Marek Maly
- [AMBER] Solvating the system with polyethylene glycol PEG Iqbal, Muhammad Sajid
- Re: [AMBER] Solvating the system with polyethylene glycol PEG ABEL Stephane 175950
- Re: [AMBER] Solvating the system with polyethylene glycol PEG Hector A. Baldoni
- Re: [AMBER] problems with paramfit Robin Betz
- Re: [AMBER] problems with paramfit Marek Maly
- Re: [AMBER] Problem on making inpcrd file 肖立
- Re: [AMBER] Problem on making inpcrd file Jason Swails
- Re: [AMBER] problems with paramfit Robin Betz
- Re: [AMBER] problems with paramfit Marek Maly
Tuesday, 29 July 2014
- [AMBER] NONBONDED_PARM_INDEX Him Shweta
- Re: [AMBER] NONBONDED_PARM_INDEX David A Case
- [AMBER] Fwd: Running PCA Nicole Ippolito
- Re: [AMBER] Running PCA Daniel Roe
- Re: [AMBER] Running PCA Daniel Roe
- [AMBER] !Help!: Normal Mode Analysis xy21hb
- Re: [AMBER] Running PCA Nicole Ippolito
- Re: [AMBER] !Help!: Normal Mode Analysis Jason Swails
Wednesday, 30 July 2014
- Re: [AMBER] Solvating the system with polyethylene glycol PEG FyD
- [AMBER] HELP Needed: AMBER12 cuda compilation ERROR Saikat Dutta chowdhury
- Re: [AMBER] HELP Needed: AMBER12 cuda compilation ERROR Jason Swails
- Re: [AMBER] NONBONDED_PARM_INDEX Shweta
- Re: [AMBER] Running PCA Nicole Ippolito
- Re: [AMBER] Running PCA Daniel Roe
- [AMBER] Parameters for SulfoTyrosine Stephane Azoulay
- Re: [AMBER] Parameters for SulfoTyrosine Brian Radak
- [AMBER] AMBER renatoac.ufpa.br
- [AMBER] erro na criação do complexo renatoac.ufpa.br
- [AMBER] erro na criação do complexo renatoac.ufpa.br
- Re: [AMBER] erro na criação do complexo Daniel Roe
- Re: [AMBER] erro na criação do complexo renatoac.ufpa.br
- Re: [AMBER] problems with paramfit Marek Maly
- [AMBER] Could not find vdW (or other) parameters for type Pedro Swagger
- [AMBER] this a very green neophyte's question. J.W. Halley
- Re: [AMBER] this a very green neophyte's question. David A Case
- Re: [AMBER] this a very green neophyte's question. Parker de Waal
Thursday, 31 July 2014
- [AMBER] How to calculate the parameters of metal ions? Jinfeng Huang
- Re: [AMBER] How to calculate the parameters of metal ions? Christina Bergonzo
- Re: [AMBER] How to calculate the parameters of metal ions? Brian Radak
- Re: [AMBER] How to calculate the parameters of metal ions? FyD
- Re: [AMBER] How to calculate the parameters of metal ions? Ken Merz
- [AMBER] Zinc parameterization Nadia Li
- [AMBER] Equilibirum/System convergence Parker de Waal
- Re: [AMBER] Equilibirum/System convergence Carlos Simmerling
- [AMBER] question about lipid tutorial Jonathan Gough
- Re: [AMBER] Problem with atommap in cpptraj Daniel Roe
- Re: [AMBER] Zinc parameterization Pengfei Li
- Re: [AMBER] this a very green neophyte's question. J.W. Halley
- Re: [AMBER] this a very green neophyte's question. Parker de Waal
- Re: [AMBER] this a very green neophyte's question. Jason Swails
- Re: [AMBER] this a very green neophyte's question. Daniel Roe
- Re: [AMBER] this a very green neophyte's question. J.W. Halley
- Re: [AMBER] Zinc parameterization Nadia Li
- Re: [AMBER] this a very green neophyte's question. Jason Swails
- Re: [AMBER] this a very green neophyte's question. J.W. Halley
- [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop Vivek Shankar Bharadwaj
- Re: [AMBER] Zinc parameterization Pengfei Li
- Re: [AMBER] this a very green neophyte's question. Jason Swails
- Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop Jason Swails
- Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop Vivek Shankar Bharadwaj
- Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop Vivek Shankar Bharadwaj
- Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop Jason Swails
- Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop Vivek Shankar Bharadwaj
- Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop Vivek Shankar Bharadwaj

Last message date: Thu Jul 31 2014 - 21:00:03 PDT
Archived on: Fri Nov 15 2024 - 05:55:02 PST

Amber Archive Jul 2014 by date