Amber Archive Aug 2015: by date

Saturday, 1 August 2015
- [AMBER] cudaMemcpy GpuBuffer::Download failed - hardware or software? Eugene Radchenko
- [AMBER] algorithm for clustering solvent molecules? Jose Borreguero
Sunday, 2 August 2015
- [AMBER] Implicit solvent simulation is unexpectedly slow 浅井賢
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed - hardware orsoftware? Eugene Radchenko
- Re: [AMBER] Implicit solvent simulation is unexpectedly slow David A Case
- Re: [AMBER] Implicit solvent simulation is unexpectedly slow 浅井賢
- [AMBER] Does the "contacts" command of cpptraj implement imaging? Jose Borreguero
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed - hardware orsoftware? Ross Walker
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed - hardwareorsoftware? Eugene Radchenko
Monday, 3 August 2015
- [AMBER] PCA: generate histogram George Tzotzos
- Re: [AMBER] Antechamber for boronic acid derivatives? David A Case
- Re: [AMBER] Does the "contacts" command of cpptraj implement imaging? Jason Swails
- Re: [AMBER] PCA: generate histogram Daniel Roe
- [AMBER] FW: PMEMD: Warning: ieee_inexact is signaling Khabiri, Morteza
- Re: [AMBER] PCA: generate histogram George Tzotzos
- Re: [AMBER] algorithm for clustering solvent molecules? Jason Swails
- Re: [AMBER] PCA: generate histogram Daniel Roe
- Re: [AMBER] PCA: generate histogram George Tzotzos
- Re: [AMBER] PCA: generate histogram Daniel Roe
- Re: [AMBER] FW: PMEMD: Warning: ieee_inexact is signaling Jason Swails
- Re: [AMBER] Does the "contacts" command of cpptraj implement imaging? Jose Borreguero
- Re: [AMBER] algorithm for clustering solvent molecules? Jose Borreguero
- Re: [AMBER] algorithm for clustering solvent molecules? Jason Swails
- Re: [AMBER] algorithm for clustering solvent molecules? Jose Borreguero
- [AMBER] Installation of AmberTools 15. Overriding earlier installation George Tzotzos
- Re: [AMBER] algorithm for clustering solvent molecules? Jason Swails
- Re: [AMBER] Installation of AmberTools 15. Overriding earlier installation Jason Swails
- Re: [AMBER] PMEMD: Warning: ieee_inexact is signaling Khabiri, Morteza
- [AMBER] MM-PBSA free energy calculation with keeping x-ray water bharat lakhani
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed - hardwareorsoftware? Ross Walker
- Re: [AMBER] MM-PBSA free energy calculation with keeping x-ray water Kenneth Huang
- Re: [AMBER] PMEMD: Warning: ieee_inexact is signaling Daniel Roe
- Re: [AMBER] MCPB.py mismatch error Eleftherios A P Lambros
- Re: [AMBER] algorithm for clustering solvent molecules? Hai Nguyen
- Re: [AMBER] algorithm for clustering solvent molecules? Jose Borreguero
- Re: [AMBER] algorithm for clustering solvent molecules? Hai Nguyen
- Re: [AMBER] algorithm for clustering solvent molecules? Jose Borreguero
- [AMBER] MM-PBSA atom types bharat lakhani
- Re: [AMBER] MM-PBSA atom types Jason Swails
- Re: [AMBER] MM-PBSA atom types bharat lakhani
- [AMBER] Bad Atom type during running MMPBSA with cobalt metal ion MOHD HOMAIDUR RAHMAN
Tuesday, 4 August 2015
- [AMBER] Trying to perform a heating MD in increments Amber mail
- [AMBER] MMPBSA.py problem Debodyuti Dutta
- Re: [AMBER] Trying to perform a heating MD in increments Abelak, Kavin
- Re: [AMBER] Antechamber for boronic acid derivatives? Michael Shokhen
- [AMBER] How to construct the Ala3 peptide shown in this picture? lipengfei_mail
- [AMBER] ired analysis: No modes data specified Kris Feher
- Re: [AMBER] How to construct the Ala3 peptide shown in this picture? Jason Swails
- Re: [AMBER] Bad Atom type during running MMPBSA with cobalt metal ion Jason Swails
- Re: [AMBER] Trying to perform a heating MD in increments Jason Swails
- Re: [AMBER] How to construct the Ala3 peptide shown in this picture? David A Case
- Re: [AMBER] MMPBSA.py problem Jason Swails
- Re: [AMBER] ired analysis: No modes data specified David A Case
- Re: [AMBER] Trying to perform a heating MD in increments Amber mail
- Re: [AMBER] MM-PBSA atom types bharat lakhani
- Re: [AMBER] MM-PBSA atom types Kenneth Huang
- Re: [AMBER] MM-PBSA atom types Jason Swails
- Re: [AMBER] ired analysis: No modes data specified Kris Feher
- Re: [AMBER] MMPBSA.py problem psu4.uic.edu
- [AMBER] PCA analysis anu chandra
- Re: [AMBER] PCA analysis Daniel Roe
- [AMBER] NaN with pmemd.cuda Joseph Baker
- Re: [AMBER] NaN with pmemd.cuda Gould, Ian R
- Re: [AMBER] Bad Atom type during running MMPBSA with cobalt metal ion MOHD HOMAIDUR RAHMAN
- Re: [AMBER] Bad Atom type during running MMPBSA with cobalt metal ion Hai Nguyen
Wednesday, 5 August 2015
- [AMBER] Regarding DNA forcefield in Amber14 Pragya Priyadarshini
- Re: [AMBER] Regarding DNA forcefield in Amber14 Vlad Cojocaru
- [AMBER] PCA: comparing PCs from different trajectories George Tzotzos
- Re: [AMBER] Regarding DNA forcefield in Amber14 Vlad Cojocaru
- Re: [AMBER] Regarding DNA forcefield in Amber14 Mahad Gatti Iou
- Re: [AMBER] Regarding DNA forcefield in Amber14 Hai Nguyen
- Re: [AMBER] Regarding DNA forcefield in Amber14 Mahad Gatti Iou
- Re: [AMBER] Regarding DNA forcefield in Amber14 Vlad Cojocaru
- Re: [AMBER] Regarding DNA forcefield in Amber14 Nhai
- [AMBER] MMPBSA_Ras-Raf complex tutorial Ruchika Bhat
- [AMBER] antechamber error Lara rajam
- [AMBER] .mdcrd to .trr conversion problem Vishal Nemaysh
- Re: [AMBER] .mdcrd to .trr conversion problem Hai Nguyen
- Re: [AMBER] .mdcrd to .trr conversion problem Hai Nguyen
- [AMBER] [cpptraj] Kullback Leibler Divergence cutoff choice Eiros Zamora, Juan
- Re: [AMBER] .mdcrd to .trr conversion problem Daniel Roe
- Re: [AMBER] [cpptraj] Kullback Leibler Divergence cutoff choice Adrian Roitberg
- Re: [AMBER] antechamber error David A Case
- Re: [AMBER] [cpptraj] Kullback Leibler Divergence cutoff choice Eiros Zamora, Juan
- Re: [AMBER] PCA: comparing PCs from different trajectories Daniel Roe
- Re: [AMBER] [cpptraj] Kullback Leibler Divergence cutoff choice Daniel Roe
- Re: [AMBER] PCA: comparing PCs from different trajectories George Tzotzos
- Re: [AMBER] PCA: comparing PCs from different trajectories Daniel Roe
- Re: [AMBER] MM-PBSA atom types bharat lakhani
- Re: [AMBER] NaN with pmemd.cuda Joseph Baker
- [AMBER] issue with 4 fs hydrogen mass repartitioning taking more time than a standard 2 fs simulation in AMBER14 George Green
- Re: [AMBER] issue with 4 fs hydrogen mass repartitioning taking more time than a standard 2 fs simulation in AMBER14 Adrian Roitberg
- Re: [AMBER] issue with 4 fs hydrogen mass repartitioning taking more time than a standard 2 fs simulation in AMBER14 Jason Swails
- Re: [AMBER] NaN with pmemd.cuda Jason Swails
- Re: [AMBER] issue with 4 fs hydrogen mass repartitioning taking more time than a standard 2 fs simulation in AMBER14 George Green
- [AMBER] Thermodynamic integration goes wrong in lambda =0 while lambda = 1 is ok!! Khabiri, Morteza
- Re: [AMBER] NaN with pmemd.cuda Joseph Baker
- [AMBER] RED Server for Altered Amino Acid Edward Kalkreuter
- Re: [AMBER] Thermodynamic integration goes wrong in lambda =0 while lambda = 1 is ok!! Ying-Chieh Sun
- Re: [AMBER] NaN with pmemd.cuda koushik kasavajhala
Thursday, 6 August 2015
- Re: [AMBER] NaN with pmemd.cuda Ross Walker
- [AMBER] large .mdcrd splitting Vishal Nemaysh
- [AMBER] could not open mdcrd file Vahid Kshani
- Re: [AMBER] could not open mdcrd file Daniel Roe
- [AMBER] Problem with cpptraj autoimage command Karolina Markowska
- Re: [AMBER] large .mdcrd splitting Daniel Roe
- Re: [AMBER] Thermodynamic integration goes wrong in lambda =0 while lambda = 1 is ok!! David A Case
- Re: [AMBER] large .mdcrd splitting David A Case
- Re: [AMBER] Problem with cpptraj autoimage command Jason Swails
- Re: [AMBER] PCA: comparing PCs from different trajectories George Tzotzos
- Re: [AMBER] Problem with cpptraj autoimage command Daniel Roe
- [AMBER] Thermodynamic integration goes wrong in lambda =0 while lambda = 1 is ok!! Khabiri, Morteza
- Re: [AMBER] PCA: comparing PCs from different trajectories Eiros Zamora, Juan
- Re: [AMBER] Thermodynamic integration goes wrong in lambda =0 while lambda = 1 is ok!! David A Case
- Re: [AMBER] large .mdcrd splitting Hai Nguyen
- [AMBER] SPAM Sarah Graham
- Re: [AMBER] NaN with pmemd.cuda Joseph Baker
- Re: [AMBER] PCA: comparing PCs from different trajectories Daniel Roe
- [AMBER] "mask" command failure Ucisik, Melek Nihan
- Re: [AMBER] "mask" command failure Hai Nguyen
- Re: [AMBER] Regarding DNA forcefield in Amber14 Thomas Cheatham
- Re: [AMBER] "mask" command failure Daniel Roe
- Re: [AMBER] "mask" command failure Hai Nguyen
- Re: [AMBER] "mask" command failure Daniel Roe
- Re: [AMBER] "mask" command failure Jason Swails
Friday, 7 August 2015
- Re: [AMBER] could not open mdcrd file Vahid Kshani
- Re: [AMBER] Regarding DNA forcefield in Amber14 Vlad Cojocaru
- Re: [AMBER] NaN with pmemd.cuda Scott Le Grand
- Re: [AMBER] Problem with cpptraj autoimage command Karolina Markowska
- [AMBER] parmch2 versus parmchk CHAMI F.
- Re: [AMBER] Problem with cpptraj autoimage command Daniel Roe
- [AMBER] awards applications open for ACS Division of Computers in Chemistry Carlos Simmerling
- Re: [AMBER] "mask" command failure Ucisik, Melek Nihan
- Re: [AMBER] Problem with cpptraj autoimage command Karolina Markowska
- [AMBER] MMPBSA error using pbsa2 shenna shearin
- Re: [AMBER] MMPBSA error using pbsa2 Ray Luo, Ph.D.
Saturday, 8 August 2015
- [AMBER] Automated restart Eugene Radchenko
- Re: [AMBER] Automated restart David A Case
- Re: [AMBER] Automated restart Eugene Radchenko
- Re: [AMBER] Automated restart Jason Swails
- [AMBER] cpptraj - RMSD Amber mail
Sunday, 9 August 2015
- Re: [AMBER] MMPBSA error using pbsa2 shenna shearin
- Re: [AMBER] cpptraj - RMSD David A Case
- Re: [AMBER] MMPBSA error using pbsa2 Kenneth Huang
- Re: [AMBER] "mask" command failure Ucisik, Melek Nihan
- Re: [AMBER] cpptraj - RMSD Amber mail
- Re: [AMBER] cpptraj - RMSD Hai Nguyen
- Re: [AMBER] cpptraj - RMSD Hai Nguyen
- Re: [AMBER] MMPBSA error using pbsa2 Ray Luo, Ph.D.
Monday, 10 August 2015
- [AMBER] cpptraj gist: Eww energies Thomas Fox
- Re: [AMBER] cpptraj gist: Eww energies Tom Kurtzman
- Re: [AMBER] cpptraj gist: Eww energies Jason Swails
- Re: [AMBER] cpptraj gist: Eww energies Nguyen, Crystal
- Re: [AMBER] cpptraj gist: Eww energies Steven Ramsey
- [AMBER] mmpbsa.py: Error George Tzotzos
- Re: [AMBER] cpptraj gist: Eww energies Daniel Roe
- Re: [AMBER] "mask" command failure Daniel Roe
- Re: [AMBER] mmpbsa.py: Error Jason Swails
- Re: [AMBER] mmpbsa.py: Error George Tzotzos
- Re: [AMBER] mmpbsa.py: Error Kenneth Huang
- Re: [AMBER] mmpbsa.py: Error George Tzotzos
- Re: [AMBER] cpptraj gist: Eww energies Tom Kurtzman
- Re: [AMBER] mmpbsa.py: Error Kenneth Huang
- Re: [AMBER] mmpbsa.py: Error George Tzotzos
- [AMBER] mmpbsa.py: Error Kenneth Huang
- Re: [AMBER] mmpbsa.py: Error George Tzotzos
- Re: [AMBER] mmpbsa.py: Error Jason Swails
Tuesday, 11 August 2015
- [AMBER] FW: Regarding AMBER 14 praSanna kuMar naYak
- [AMBER] FW: Regarding AMBER14 Error praSanna kuMar naYak
- [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Sangita Kachhap
- [AMBER] AMBER 14 installation Problem Himansu
- Re: [AMBER] FW: Regarding AMBER 14 David A Case
- Re: [AMBER] FW: Regarding AMBER14 Error David A Case
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Jason Swails
- Re: [AMBER] FW: Regarding AMBER 14 praSanna kuMar naYak
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Sangita Kachhap
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Jason Swails
- Re: [AMBER] FW: Regarding AMBER 14 Kenneth Huang
- Re: [AMBER] FW: Regarding AMBER 14 Jason Swails
- Re: [AMBER] FW: Regarding AMBER 14 praSanna kuMar naYak
- Re: [AMBER] FW: Regarding AMBER 14 Jason Swails
- Re: [AMBER] SPAM Jason Swails
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Sangita Kachhap
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Jason Swails
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Sangita Kachhap
- Re: [AMBER] "mask" command failure Ucisik, Melek Nihan
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Jason Swails
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Sangita Kachhap
- [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Amber mail
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Jason Swails
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Amber mail
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Adrian Roitberg
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Daniel Roe
- Re: [AMBER] "mask" command failure Daniel Roe
- [AMBER] using chamber to convert psf to prmtop KK R
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Amber mail
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Jason Swails
- Re: [AMBER] using chamber to convert psf to prmtop Jason Swails
- [AMBER] Macromolecular crowding force-field and parameters richa anand
Wednesday, 12 August 2015
- Re: [AMBER] FW: Regarding AMBER 14 praSanna kuMar naYak
- Re: [AMBER] FW: Regarding AMBER 14 Jason Swails
- Re: [AMBER] FW: Regarding AMBER 14 praSanna kuMar naYak
- [AMBER] acetylate and ammoniate mohammad r
- Re: [AMBER] acetylate and ammoniate Jason Swails
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Amber mail
- [AMBER] Warning: ieee_inexact is signaling PMEMD Terminated Abnormally! Khabiri, Morteza
- [AMBER] cpptraj frames clustering limit Gaurao Dhoke
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Jason Swails
- Re: [AMBER] cpptraj frames clustering limit Amber mail
- Re: [AMBER] cpptraj frames clustering limit Jason Swails
- Re: [AMBER] acetylate and ammoniate mohammad r
- Re: [AMBER] cpptraj frames clustering limit Daniel Roe
- Re: [AMBER] Warning: ieee_inexact is signaling PMEMD Terminated Abnormally! Daniel Roe
- Re: [AMBER] cpptraj gist: Eww energies Thomas Fox
- [AMBER] GIST vs. 3D-RISM Thomas Fox
- Re: [AMBER] acetylate and ammoniate David A Case
- Re: [AMBER] Warning: ieee_inexact is signaling PMEMD Terminated Abnormally! Khabiri, Morteza
- Re: [AMBER] Warning: ieee_inexact is signaling PMEMD Terminated Abnormally! Daniel Roe
- Re: [AMBER] GIST vs. 3D-RISM Nguyen, Crystal
- Re: [AMBER] Warning: ieee_inexact is signaling PMEMD Terminated Abnormally! Khabiri, Morteza
- Re: [AMBER] GIST vs. 3D-RISM Tyler Luchko (Lists)
- [AMBER] cg in GAFF: amb2gmx.pl vs virtualchemistry - LJ well depth Sharapa
- Re: [AMBER] cg in GAFF: amb2gmx.pl vs virtualchemistry - LJ well depth David A Case
- [AMBER] amber14 gpu webpage lists cuda 7.0 as supported Dow Hurst
- [AMBER] [Solved] amber14 gpu webpage lists cuda 7.0 as supported Dow Hurst
- Re: [AMBER] amber14 gpu webpage lists cuda 7.0 as supported diane lynch
- Re: [AMBER] [Solved] amber14 gpu webpage lists cuda 7.0 as supported diane lynch
- Re: [AMBER] Macromolecular crowding force-field and parameters Lijuan Yu
- [AMBER] Force-field and parameters richa anand
- [AMBER] pH-REMD theory whb
Thursday, 13 August 2015
- Re: [AMBER] acetylate and ammoniate mohammad r
- Re: [AMBER] cpptraj frames clustering limit Gaurao Dhoke
- [AMBER] MMPBSA.py error Urszula Uciechowska
- Re: [AMBER] acetylate and ammoniate Jason Swails
- [AMBER] Imaging and connectivity error Harmeet Kaur
- Re: [AMBER] pH-REMD theory Jason Swails
- Re: [AMBER] Imaging and connectivity error Jason Swails
- [AMBER] dynlmb and TI Khabiri, Morteza
- Re: [AMBER] cpptraj frames clustering limit Daniel Roe
- [AMBER] ImportError: No module named mcpb.gene_model_files Marcelo Andrade Chagas
- [AMBER] Job submission script for SGE Himansu
- [AMBER] The protein is Leaving the water box! Amber mail
Friday, 14 August 2015
- [AMBER] help in rdf Robin Jain
- Re: [AMBER] The protein is Leaving the water box! Jason Swails
- Re: [AMBER] Job submission script for SGE Jason Swails
- Re: [AMBER] Job submission script for SGE Gerald Monard
- Re: [AMBER] The protein is Leaving the water box! Amber mail
- Re: [AMBER] The protein is Leaving the water box! Jason Swails
- Re: [AMBER] help in rdf Daniel Roe
- [AMBER] the better box size Investigador Química
- Re: [AMBER] the better box size Jason Swails
- Re: [AMBER] the better box size Bill Ross
Saturday, 15 August 2015
- [AMBER] RMSD and average value of interatomic distance? Michael Shokhen
- Re: [AMBER] AMBER Digest, Vol 1311, Issue 1 Robin Jain
- Re: [AMBER] RMSD and average value of interatomic distance? Jason Swails
- Re: [AMBER] AMBER Digest, Vol 1311, Issue 1 Jason Swails
- Re: [AMBER] RMSD and average value of interatomic distance? Michael Shokhen
- Re: [AMBER] RMSD and average value of interatomic distance? Adrian Roitberg
- Re: [AMBER] RMSD and average value of interatomic distance? Michael Shokhen
- Re: [AMBER] RMSD and average value of interatomic distance? Daniel Roe
- Re: [AMBER] RMSD and average value of interatomic distance? Michael Shokhen
- [AMBER] About the QMMM simulation with LIO software Yeng-Tseng Wang
- Re: [AMBER] About the QMMM simulation with LIO software Jason Swails
Sunday, 16 August 2015
- [AMBER] A query about MMPBSA.py calcualtion anu chandra
- Re: [AMBER] A query about MMPBSA.py calcualtion Jason Swails
- [AMBER] ****** in results? Chinh Su Tran To
Monday, 17 August 2015
- [AMBER] error running mmpbsa.pl Urszula Uciechowska
- Re: [AMBER] error running mmpbsa.pl Urszula Uciechowska
- [AMBER] Help needed regarding simulating Lipopolysaccharide Mrinda Jones
- [AMBER] STOP PMEMD Terminated Abnormally! Pragya Priyadarshini
- Re: [AMBER] ****** in results? David A Case
- Re: [AMBER] Help needed regarding simulating Lipopolysaccharide David A Case
- Re: [AMBER] STOP PMEMD Terminated Abnormally! David A Case
- Re: [AMBER] ImportError: No module named mcpb.gene_model_files Marcelo Andrade Chagas
- Re: [AMBER] Help needed regarding simulating Lipopolysaccharide Mrinda Jones
- [AMBER] saveamberparm mohammad r
- Re: [AMBER] STOP PMEMD Terminated Abnormally! Pragya Priyadarshini
- Re: [AMBER] saveamberparm Daniel Roe
- Re: [AMBER] ImportError: No module named mcpb.gene_model_files Daniel Roe
- Re: [AMBER] Help needed regarding simulating Lipopolysaccharide Lachele Foley
- Re: [AMBER] saveamberparm David A Case
- Re: [AMBER] ImportError: No module named mcpb.gene_model_files Marcelo Andrade Chagas
- Re: [AMBER] About the QMMM simulation with LIO software Yeng-Tseng Wang
- Re: [AMBER] About the QMMM simulation with LIO software Jason Swails
- Re: [AMBER] STOP PMEMD Terminated Abnormally! Jason Swails
- Re: [AMBER] About the QMMM simulation with LIO software Adrian Roitberg
- [AMBER] Big potential difference between conformation in MD simulation and optimized conformation in Gaussian. Eg eh
- [AMBER] calculation of rmsd with cpptraj Krantzman, Kristin D
- Re: [AMBER] calculation of rmsd with cpptraj Jason Swails
- Re: [AMBER] Big potential difference between conformation in MD simulation and optimized conformation in Gaussian. Bill Ross
- Re: [AMBER] calculation of rmsd with cpptraj Krantzman, Kristin D
- Re: [AMBER] Big potential difference between conformation in MD simulation and optimized conformation in Gaussian. Jason Swails
- Re: [AMBER] saveamberparm mohammad r
- [AMBER] cpptraj cluster in MPI Lara rajam
- Re: [AMBER] cpptraj cluster in MPI Kenneth Huang
- Re: [AMBER] cpptraj cluster in MPI Lara rajam
- Re: [AMBER] cpptraj cluster in MPI Daniel Roe
- [AMBER] Immediate PhD Opening In Computational Structural Biology Of Membrane Proteins Marawan Hussien
- [AMBER] Immediate Postdoctoral Position Opening In Computational Chemistry And Computer-Aided Drug Design (CADD) Marawan Hussien
- Re: [AMBER] STOP PMEMD Terminated Abnormally! Pragya Priyadarshini
- [AMBER] acpype mohammad r
Tuesday, 18 August 2015
- Re: [AMBER] About the QMMM simulation with LIO software Yeng-Tseng Wang
- Re: [AMBER] About the QMMM simulation with LIO software Yeng-Tseng Wang
- [AMBER] acpype mohammad r
- [AMBER] ancpype problem mohammad r
- [AMBER] Total interaction energy between monomeric units of a dimer anu chandra
- [AMBER] converting amber files mohammad r
- Re: [AMBER] converting amber files George Tzotzos
- Re: [AMBER] converting amber files Jason Swails
- [AMBER] NPT equilibration failed Albert
- Re: [AMBER] NPT equilibration failed Adrian Roitberg
- Re: [AMBER] Total interaction energy between monomeric units of a dimer Daniel Roe
- Re: [AMBER] Total interaction energy between monomeric units of a dimer Jason Swails
- Re: [AMBER] NPT equilibration failed Albert
- Re: [AMBER] converting amber files mohammad r
- Re: [AMBER] converting amber files Jason Swails
- Re: [AMBER] acpype David A Case
- [AMBER] hpc error Damiano Spadoni
- [AMBER] cpptraj RMSD stats George Tzotzos
- Re: [AMBER] converting amber files mohammad r
- Re: [AMBER] cpptraj RMSD stats Daniel Roe
- Re: [AMBER] acpype mohammad r
- Re: [AMBER] hpc error David A Case
- Re: [AMBER] Total interaction energy between monomeric units of a dimer anu chandra
- Re: [AMBER] converting amber files Kenneth Huang
- Re: [AMBER] acpype Suman Chakrabarty
- Re: [AMBER] converting amber files Jason Swails
- [AMBER] cpptraj perress RMSD George Tzotzos
- Re: [AMBER] cpptraj perress RMSD Daniel Roe
- Re: [AMBER] converting amber files mohammad r
- Re: [AMBER] cpptraj RMSD stats George Tzotzos
- Re: [AMBER] cpptraj RMSD stats Daniel Roe
- [AMBER] upgrading to AT15 (from AT14) Massimiliano Porrini
- Re: [AMBER] cpptraj perress RMSD George Tzotzos
- Re: [AMBER] upgrading to AT15 (from AT14) Jason Swails
- Re: [AMBER] upgrading to AT15 (from AT14) David A Case
- [AMBER] adding NaCl mohammad r
- [AMBER] adding NaCl mohammad r
- Re: [AMBER] upgrading to AT15 (from AT14) mohammad r
Wednesday, 19 August 2015
- [AMBER] CL topology Albert
- Re: [AMBER] Help needed regarding simulating Lipopolysaccharide Mrinda Jones
- [AMBER] adding NaCl mohammad r
- Re: [AMBER] adding NaCl Bill Ross
- Re: [AMBER] adding NaCl mohammad r
- Re: [AMBER] adding NaCl Jason Swails
- Re: [AMBER] CL topology Jason Swails
- [AMBER] RESP fitting Mahmood Jasim
- Re: [AMBER] the better box size for calculating host-guest interaction energies Investigador Química
- Re: [AMBER] Help needed regarding simulating Lipopolysaccharide David A Case
- Re: [AMBER] RESP fitting David A Case
- Re: [AMBER] the better box size for calculating host-guest interaction energies Jason Swails
- Re: [AMBER] Total interaction energy between monomeric units of a dimer George Tzotzos
- Re: [AMBER] Total interaction energy between monomeric units of a dimer David A Case
- Re: [AMBER] RESP fitting cieplak.cgl.ucsf.edu
- [AMBER] xleap numbering in residues Lara rajam
Thursday, 20 August 2015
- Re: [AMBER] Total interaction energy between monomeric units of a dimer anu chandra
- Re: [AMBER] xleap numbering in residues David A Case
- Re: [AMBER] Total interaction energy between monomeric units of a dimer David A Case
- Re: [AMBER] Total interaction energy between monomeric units of a dimer Hector A. Baldoni
- Re: [AMBER] Total interaction energy between monomeric units of a dimer Jason Swails
- Re: [AMBER] Total interaction energy between monomeric units of a dimer Hector A. Baldoni
- Re: [AMBER] the better box size for calculating host-guest interaction energies Investigador Química
- Re: [AMBER] the better box size for calculating host-guest interaction energies Jason Swails
- Re: [AMBER] RESP fitting Mahmood Jasim
- Re: [AMBER] the better box size for calculating host-guest interaction energies David A Case
- [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ anu chandra
- Re: [AMBER] the better box size for calculating host-guest interaction energies Adrian Roitberg
- Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ Jason Swails
- [AMBER] Problem with using the 12-6-4 LJ-Type Nonbonded Model in a an RNA-Mg system Kasprzak, Wojciech (NIH/NCI) [C]
- [AMBER] Using MMPBSA.py with CHARMM force field Ara Abramyan
- [AMBER] hydrogen mass repartitioning visualization in chimera George Green
- Re: [AMBER] hydrogen mass repartitioning visualization in chimera Adrian Roitberg
- Re: [AMBER] hydrogen mass repartitioning visualization in chimera George Green
- Re: [AMBER] hydrogen mass repartitioning visualization in chimera George Green
- Re: [AMBER] hydrogen mass repartitioning visualization in chimera Nhai
- Re: [AMBER] hydrogen mass repartitioning visualization in chimera George Green
Friday, 21 August 2015
- Re: [AMBER] upgrading to AT15 (from AT14) Massimiliano Porrini
- Re: [AMBER] upgrading to AT15 (from AT14) David A Case
- Re: [AMBER] hydrogen mass repartitioning visualization in chimera Jason Swails
- Re: [AMBER] Using MMPBSA.py with CHARMM force field Jason Swails
- Re: [AMBER] hydrogen mass repartitioning visualization in chimera George Green
- [AMBER] Autoimage Warning Brittany Boykin
- Re: [AMBER] Using MMPBSA.py with CHARMM force field David A Case
- Re: [AMBER] ImportError: No module named mcpb.gene_model_files Marcelo Andrade Chagas
- Re: [AMBER] ImportError: No module named mcpb.gene_model_files Jason Swails
- Re: [AMBER] Autoimage Warning Jason Swails
- Re: [AMBER] ImportError: No module named mcpb.gene_model_files Marcelo Andrade Chagas
- Re: [AMBER] Using MMPBSA.py with CHARMM force field Ara Abramyan
- Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ anu chandra
- Re: [AMBER] ImportError: No module named mcpb.gene_model_files David A Case
- Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ David A Case
- Re: [AMBER] Using MMPBSA.py with CHARMM force field Jason Swails
- [AMBER] closest command in cpptraj Joseph Baker
- Re: [AMBER] closest command in cpptraj Daniel Roe
- [AMBER] help in density equilibration Robin Jain
Saturday, 22 August 2015
- Re: [AMBER] the better box size for calculating host-guest interaction energies Investigador Química
- Re: [AMBER] the better box size for calculating host-guest interaction energies Investigador Química
- Re: [AMBER] the better box size for calculating host-guest interaction energies Investigador Química
- [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces Parker de Waal
Sunday, 23 August 2015
- [AMBER] adding lipid mohammad r
- [AMBER] how to add lipid mohammad r
- [AMBER] how to add lipid mohammad roostaie
- [AMBER] tleap ask for bond to zinc ion Jorgen Simonsen
- Re: [AMBER] how to add lipid Bill Ross
- Re: [AMBER] tleap ask for bond to zinc ion Bill Ross
- [AMBER] help in density equilibration Robin Jain
- [AMBER] Regarding No of Hydrogen bonds (vs) Residue wise Garisekurthi Satheesh
- Re: [AMBER] how to add lipid mohammad r
- Re: [AMBER] how to add lipid Bill Ross
- Re: [AMBER] help in density equilibration Bill Ross
Monday, 24 August 2015
- Re: [AMBER] how to add lipid mohammad r
- Re: [AMBER] upgrading to AT15 (from AT14) Massimiliano Porrini
- Re: [AMBER] tleap ask for bond to zinc ion David A Case
- Re: [AMBER] help in density equilibration David A Case
- Re: [AMBER] upgrading to AT15 (from AT14) David A Case
- Re: [AMBER] closest command in cpptraj Joseph Baker
- Re: [AMBER] Regarding No of Hydrogen bonds (vs) Residue wise Daniel Roe
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces Ross Walker
- Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ George Tzotzos
- [AMBER] AMBER Autoimage Warning Brittany Boykin
- Re: [AMBER] how to add lipid mohammad r
- Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ Jason Swails
- Re: [AMBER] Regarding No of Hydrogen bonds (vs) Residue wise Hai Nguyen
- Re: [AMBER] how to add lipid mohammad r
- Re: [AMBER] tleap ask for bond to zinc ion Marcelo Andrade Chagas
- Re: [AMBER] AMBER Autoimage Warning Jason Swails
- Re: [AMBER] how to add lipid Jason Swails
- Re: [AMBER] how to add lipid Jason Swails
- Re: [AMBER] AMBER Autoimage Warning Daniel Roe
- Re: [AMBER] how to add lipid mohammad r
- Re: [AMBER] Regarding No of Hydrogen bonds (vs) Residue wise Garisekurthi Satheesh
- Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ George Tzotzos
- Re: [AMBER] how to add lipid Bill Ross
- Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ Jason Swails
- Re: [AMBER] closest command in cpptraj Joseph Baker
- Re: [AMBER] closest command in cpptraj Joseph Baker
- Re: [AMBER] closest command in cpptraj Hai Nguyen
- [AMBER] ImportError: No module named scipy.optimize Sushi Shilpa
- Re: [AMBER] ImportError: No module named scipy.optimize Nhai
- Re: [AMBER] how to add lipid mohammad r
- Re: [AMBER] how to add lipid mohammad r
- [AMBER] how to neutralized my system with Na+ ions Martina Devi
Tuesday, 25 August 2015
- [AMBER] Regarding printing of trajectory MOHD HOMAIDUR RAHMAN
- Re: [AMBER] how to add lipid Bill Ross
- Re: [AMBER] how to add lipid mohammad r
- Re: [AMBER] how to add lipid mohammad r
- [AMBER] mismatch base pair from nab Martina Devi
- Re: [AMBER] mismatch base pair from nab Carlos Simmerling
- [AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids anilkumarsahoo.physics.iisc.ernet.in
- Re: [AMBER] how to neutralized my system with Na+ ions David A Case
- Re: [AMBER] Regarding printing of trajectory David A Case
- Re: [AMBER] how to neutralized my system with Na+ ions Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] mismatch base pair from nab Martina Devi
- Re: [AMBER] mismatch base pair from nab Carlos Simmerling
- Re: [AMBER] closest command in cpptraj Daniel Roe
- Re: [AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids Daniel Roe
- Re: [AMBER] how to neutralized my system with Na+ ions Martina Devi
- Re: [AMBER] how to neutralized my system with Na+ ions Jason Swails
- Re: [AMBER] Regarding printing of trajectory MOHD HOMAIDUR RAHMAN
- Re: [AMBER] how to neutralized my system with Na+ ions Martina Devi
- Re: [AMBER] Regarding printing of trajectory Daniel Roe
- Re: [AMBER] how to neutralized my system with Na+ ions Martina Devi
- Re: [AMBER] how to add lipid Charles Lin
- Re: [AMBER] how to neutralized my system with Na+ ions Jason Swails
- Re: [AMBER] how to neutralized my system with Na+ ions Hai Nguyen
- [AMBER] Non-equilibrium pulling with plane-point restraints Jacob Monroe
- Re: [AMBER] Regarding printing of trajectory MOHD HOMAIDUR RAHMAN
- Re: [AMBER] mismatch base pair from nab David A Case
- Re: [AMBER] how to add lipid Bill Ross
- [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein Wenyu Qian
- [AMBER] cpin error Arjun Sharma
- Re: [AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids anilkumarsahoo.physics.iisc.ernet.in
- Re: [AMBER] closest command in cpptraj Joseph Baker
Wednesday, 26 August 2015
- Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein David A Case
- Re: [AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids David A Case
- Re: [AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids Jason Swails
- Re: [AMBER] cpin error Jason Swails
- Re: [AMBER] how to add lipid mohammad r
- Re: [AMBER] how to add lipid mohammad r
- Re: [AMBER] closest command in cpptraj Daniel Roe
- Re: [AMBER] Total interaction energy between monomeric units of a dimer anu chandra
- Re: [AMBER] Total interaction energy between monomeric units of a dimer Jason Swails
Thursday, 27 August 2015
- Re: [AMBER] Non-equilibrium pulling with plane-point restraints achim.sandmann.chemie.stud.uni-erlangen.de
- [AMBER] Does it mean the card is damaged? Karolina Markowska
- [AMBER] Charge-dependent exchange-dispersion corrections Lucas A. Defelipe
- [AMBER] Molsurf: some questions on usage George Tzotzos
- Re: [AMBER] Does it mean the card is damaged? Ross Walker
- Re: [AMBER] Cpin error Arjun Sharma
- Re: [AMBER] Cpin error Jason Swails
- Re: [AMBER] how to add lipid Charles Lin
- Re: [AMBER] Non-equilibrium pulling with plane-point restraints Jacob Monroe
- Re: [AMBER] how to add lipid Repic Matej
- Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein Mohammad Salem
- Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein Bill Ross
- [AMBER] Looking for suggestion for analysis Mohd Farid Ismail
Friday, 28 August 2015
- Re: [AMBER] how to add lipid mohammad r
- Re: [AMBER] Does it mean the card is damaged? Karolina Markowska
- Re: [AMBER] Non-equilibrium pulling with plane-point restraints achim.sandmann.chemie.stud.uni-erlangen.de
- Re: [AMBER] hpc error Damiano Spadoni
- Re: [AMBER] Molsurf: some questions on usage David A Case
- Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein David A Case
- Re: [AMBER] hpc error David A Case
- Re: [AMBER] how to add lipid Jason Swails
- Re: [AMBER] cpin error Arjun Sharma
- Re: [AMBER] cpin error Jason Swails
- Re: [AMBER] how to add lipid mohammad r
- Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein Wenyu Qian
- Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein David A Case
- [AMBER] Confusion in running QM/MMGBSA MOHD HOMAIDUR RAHMAN
- Re: [AMBER] Confusion in running QM/MMGBSA David A Case
Saturday, 29 August 2015
- [AMBER] How do I study the dimerisation energy (i.e. energy required to form a dimer from two monomeric units) using AMBER? Suchetana Gupta
- [AMBER] Segmentation Fault with pmemd Ziheng Wang
- Re: [AMBER] Confusion in running QM/MMGBSA Jason Swails
- Re: [AMBER] Segmentation Fault with pmemd Jason Swails
- Re: [AMBER] How do I study the dimerisation energy (i.e. energy required to form a dimer from two monomeric units) using AMBER? David A Case
- Re: [AMBER] Segmentation Fault with pmemd David A Case
- Re: [AMBER] mismatch base pair from nab Martina Devi
Sunday, 30 August 2015
- Re: [AMBER] Segmentation Fault with pmemd Ziheng Wang
- Re: [AMBER] Segmentation Fault with pmemd David A Case
- [AMBER] cyclic peptides Lara rajam
- Re: [AMBER] cyclic peptides David A Case
Monday, 31 August 2015
- Re: [AMBER] Does it mean the card is damaged? Karolina Markowska
- [AMBER] job submission in RED Martina Devi
- [AMBER] Thermodynamic integration and segmentation fault Khabiri, Morteza
- Re: [AMBER] Does it mean the card is damaged? Ross Walker
- [AMBER] Draw a cube around the molecules Iqbal, Muhammad Sajid
- Re: [AMBER] Draw a cube around the molecules Lorenzo Gontrani
- Re: [AMBER] Draw a cube around the molecules Jason Swails
- Re: [AMBER] Draw a cube around the molecules Repic Matej
- Re: [AMBER] Non-equilibrium pulling with plane-point restraints Jacob Monroe

Last message date: Mon Aug 31 2015 - 17:00:03 PDT
Archived on: Mon Nov 03 2025 - 05:55:13 PST

Amber Archive Aug 2015 by date