Amber Archive May 2012: by date

Monday, 30 April 2012
- Re: [AMBER] getting metal ions coordinates of nmr structures of a protein Daniel Sindhikara
Tuesday, 1 May 2012
- Re: [AMBER] input format for qms Jason Swails
- [AMBER] Some problem with building Non-standard residue Nicholus Bhattacharjee
- Re: [AMBER] error in decomposition analysis using ambertools 1.5 Jason Swails
- Re: [AMBER] using two GPUs Robert Crovella
- Re: [AMBER] using two GPUs Shaw, Sharon
- Re: [AMBER] using two GPUs Scott Le Grand
- Re: [AMBER] Amber 12 Installation errors relevant to fftw3 Shulin Zhuang
- Re: [AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration Marek Maly
- Re: [AMBER] mbondi3 Hai Nguyen
Wednesday, 2 May 2012
- Re: [AMBER] Some problem with building Non-standard residue FyD
- Re: [AMBER] error in decomposition analysis using ambertools 1.5 Kumar, Sonu
- [AMBER] anisotropic pressure in bilayer simulation Vijay Manickam Achari
- [AMBER] what's the difference between sandar.MPI and sander.LES.MPI ? Albert
- Re: [AMBER] using two GPUs Ross Walker
- Re: [AMBER] what's the difference between sandar.MPI and sander.LES.MPI ? Ross Walker
- [AMBER] Electrostatic potential calculation Sudarshan Debnath
- [AMBER] Umbrella sampling using GPU acceleration Massimiliano Porrini
- Re: [AMBER] Umbrella sampling using GPU acceleration Ross Walker
- Re: [AMBER] anisotropic pressure in bilayer simulation Ross Walker
- Re: [AMBER] Radii in prmtop Jesper Sørensen
- Re: [AMBER] mbondi3 Jesper Sørensen
- Re: [AMBER] anisotropic pressure in bilayer simulation Benjamin D Madej
- [AMBER] Fwd: Electrostatic potential calculation Ray Luo, Ph.D.
- Re: [AMBER] error in decomposition analysis using ambertools 1.5 Jason Swails
- Re: [AMBER] Electrostatic potential calculation Qin Cai
- Re: [AMBER] mbondi3 Jason Swails
- [AMBER] Energy Differences between mmpbsa_py_energy and sander outputs Damodaran, Komath
- Re: [AMBER] error in decomposition analysis using ambertools 1.5 Kumar, Sonu
- [AMBER] RESP structure optimization for larger ligand Robin Betz
- Re: [AMBER] mbondi3 Jesper Soerensen
- Re: [AMBER] using two GPUs Vijay Manickam Achari
- Re: [AMBER] error in decomposition analysis using ambertools 1.5 Jason Swails
- Re: [AMBER] mbondi3 Jason Swails
- [AMBER] using two GPUs Vijay Manickam Achari
- [AMBER] a question about ensemble Albert
- [AMBER] Max Pairlist Cutoff issue Agostino Bruno
Thursday, 3 May 2012
- Re: [AMBER] using two GPUs Ross Walker
- [AMBER] adding/deleting water molecules in leap Bala subramanian
- Re: [AMBER] adding/deleting water molecules in leap Simon Becker
- [AMBER] CHAMBER with RNA Sean Law
- Re: [AMBER] mbondi3 Jesper Sørensen
- Re: [AMBER] Max Pairlist Cutoff issue Aron Broom
- Re: [AMBER] RESP structure optimization for larger ligand Dean Cuebas
- [AMBER] Amber 11, Amber-Tools 1.5 and Amber-Tools 12 respgen Bug Marko Wehle
- Re: [AMBER] a question about ensemble Benjamin D Madej
- Re: [AMBER] a question about ensemble case
- [AMBER] Building Amber 12 & python Shaw, Sharon
- Re: [AMBER] Building Amber 12 & python case
- [AMBER] MCPB espgen error Fabrício Bracht
- Re: [AMBER] mbondi3 Jesper Sørensen
- [AMBER] am1d problem Gabriel Jara
- Re: [AMBER] adding/deleting water molecules in leap Jason Swails
- Re: [AMBER] adding/deleting water molecules in leap Jason Swails
- Re: [AMBER] mbondi3 case
- [AMBER] Fwd: question pooja chahal
- [AMBER] question pooja chahal
- [AMBER] Amber10 parallel test Shaandar Nyamtulga
- Re: [AMBER] question mish
- Re: [AMBER] Some problem with building Non-standard residue Nicholus Bhattacharjee
Friday, 4 May 2012
- Re: [AMBER] question steinbrt.rci.rutgers.edu
- Re: [AMBER] Amber 11, Amber-Tools 1.5 and Amber-Tools 12 respgen Bug FyD
- Re: [AMBER] RESP structure optimization for larger ligand FyD
- [AMBER] ptraj closest water script problem Andre Serobian
- Re: [AMBER] ptraj closest water script problem Thomas Cheatham
- [AMBER] mmpbsa problem . mirage
- Re: [AMBER] ptraj closest water script problem Daniel Roe
- [AMBER] Why not AmberTools12 bugfix.all Alan
- Re: [AMBER] Why not AmberTools12 bugfix.all Alan
- Re: [AMBER] Fwd: question David A Case
- Re: [AMBER] Amber10 parallel test David A Case
- Re: [AMBER] Some problem with building Non-standard residue FyD
- Re: [AMBER] Why not AmberTools12 bugfix.all Jason Swails
- Re: [AMBER] mmpbsa problem Ray Luo, Ph.D.
- [AMBER] add H-atoms automatic in tleap Zhou Gong
- Re: [AMBER] Amber 11, Amber-Tools 1.5 and Amber-Tools 12 respgen Bug Marko Wehle
- Re: [AMBER] add H-atoms automatic in tleap David A Case
- Re: [AMBER] Building Amber 12 & python Shaw, Sharon
Saturday, 5 May 2012
- Re: [AMBER] Amber 11, Amber-Tools 1.5 and Amber-Tools 12 respgen Bug FyD
- Re: [AMBER] Amber 11, Amber-Tools 1.5 and Amber-Tools 12 respgen Bug case
- Re: [AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration case
- [AMBER] 答复: add H-atoms automatic in tleap Zhou Gong
- Re: [AMBER] 答复: add H-atoms automatic in tleap case
- [AMBER] 答复: 答复: add H-atoms automatic in tleap Zhou Gong
- Re: [AMBER] Max Pairlist Cutoff issue Ben Roberts
Sunday, 6 May 2012
- Re: [AMBER] : add H-atoms automatic in tleap FyD
- Re: [AMBER] 答复: 答复: add H-atoms automatic in tleap case
- [AMBER] A1. Conversion of Gaussian output into mol 2 file Debolina Mitra
- [AMBER] 答复: 答复: 答复: add H-atoms automatic in tleap Zhou Gong
- Re: [AMBER] A1. Conversion of Gaussian output into mol 2 file case
- Re: [AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration Marek Maly
- Re: [AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration David Case
- Re: [AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration Marek Maly
- [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? Marek Maly
- [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined Mark Rance
- Re: [AMBER] ptraj closest water script problem Andre Serobian
- Re: [AMBER] A1. Conversion of Gaussian output into mol 2 file Nadine Homeyer
- [AMBER] strange CUDA MD output in VMD Albert
- Re: [AMBER] A1. Conversion of Gaussian output into mol 2 file FyD
- [AMBER] MMPBSA calculation of large proteins Jyotsna Bhat
Monday, 7 May 2012
- Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? steinbrt.rci.rutgers.edu
- [AMBER] Homotrimeric structure not holding together during equilibration steps an MD simulations. Emilio Lence
- Re: [AMBER] Homotrimeric structure not holding together during equilibration steps an MD simulations. Carlos Simmerling
- Re: [AMBER] strange CUDA MD output in VMD Daniel Roe
- Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined David A Case
- [AMBER] PLEASE GIVE SOME SUGGESTION jit mukherjee
- Re: [AMBER] PLEASE GIVE SOME SUGGESTION steinbrt.rci.rutgers.edu
- Re: [AMBER] strange CUDA MD output in VMD Albert
- Re: [AMBER] MMPBSA calculation of large proteins Jason Swails
- [AMBER] MCPB espgen error Fabrício Bracht
- Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? Marek Maly
- Re: [AMBER] MMPBSA calculation of large proteins Jyotsna Bhat
- Re: [AMBER] PLEASE GIVE SOME SUGGESTION jit mukherjee
- Re: [AMBER] MMPBSA calculation of large proteins Ray Luo, Ph.D.
- Re: [AMBER] PLEASE GIVE SOME SUGGESTION David A Case
- [AMBER] intel compiler still doesn't work for MPI Albert
- [AMBER] error when using PMEMD Chris Chris
- Re: [AMBER] intel compiler still doesn't work for MPI Jason Swails
- Re: [AMBER] error when using PMEMD Jason Swails
- Re: [AMBER] intel compiler still doesn't work for MPI Albert
- Re: [AMBER] PLEASE GIVE SOME SUGGESTION jit mukherjee
- Re: [AMBER] MCPB espgen error Ben Roberts
- [AMBER] CUDA running error Albert
- Re: [AMBER] MCPB espgen error Fabrício Bracht
- Re: [AMBER] am1d problem Andreas Goetz
- Re: [AMBER] MCPB espgen error FyD
- [AMBER] error with torus in ffgbsa Charlotte Siska
- [AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 ) Yeng-Tseng Wang
- [AMBER] help with pmemd .in file Chris Chris
- Re: [AMBER] help with pmemd .in file Niel Henriksen
- Re: [AMBER] error with torus in ffgbsa case
- Re: [AMBER] help with pmemd .in file Jason Swails
- Re: [AMBER] help with pmemd .in file Chris Chris
- Re: [AMBER] help with pmemd .in file Chris Chris
- Re: [AMBER] help with pmemd .in file Niel Henriksen
- Re: [AMBER] PLEASE GIVE SOME SUGGESTION jit mukherjee
- Re: [AMBER] MCPB espgen error Fabrício Bracht
- [AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 ) c00jsw00.nchc.narl.org.tw
- Re: [AMBER] PLEASE GIVE SOME SUGGESTION Jyotsna Bhat
- [AMBER] CUDA running error Albert
- [AMBER] Sander Error Melissa Buskes
- [AMBER] CUDA test failed Albert
Tuesday, 8 May 2012
- [AMBER] strange CUDA benchmark Albert
- [AMBER] apply an external force between two residue mehdi bagherpoor
- [AMBER] high value in MMPBSA xiaojiong
- [AMBER] charmmlipid2amber.x error Albert
- Re: [AMBER] MMPBSA calculation of large proteins Jyotsna Bhat
- Re: [AMBER] CHAMBER with RNA Mark Williamson
- Re: [AMBER] high value in MMPBSA Bill Miller III
- Re: [AMBER] help with pmemd .in file David A Case
- Re: [AMBER] PLEASE GIVE SOME SUGGESTION David A Case
- Re: [AMBER] Sander Error David A Case
- Re: [AMBER] charmmlipid2amber.x error David A Case
- Re: [AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 ) Brian Radak
- Re: [AMBER] charmmlipid2amber.x error Albert
- Re: [AMBER] charmmlipid2amber.x error Albert
- [AMBER] job terminate abnormally Albert
- [AMBER] Error while loading file in VMD kirtana S
- Re: [AMBER] job terminate abnormally Marc van der Kamp
- Re: [AMBER] job terminate abnormally Jason Swails
- Re: [AMBER] job terminate abnormally Jason Swails
- Re: [AMBER] job terminate abnormally Albert
- [AMBER] error in SMD mehdi bagherpoor
- Re: [AMBER] high value in MMPBSA 21119012
- [AMBER] non-polar solvation energies decomposed in PB Qiong Zhang
- Re: [AMBER] help with pmemd .in file Chris Chris
- Re: [AMBER] MMPBSA calculation of large proteins Ray Luo, Ph.D.
- Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? steinbrt.rci.rutgers.edu
- Re: [AMBER] help with pmemd .in file Ross Walker
- Re: [AMBER] high value in MMPBSA Ray Luo, Ph.D.
- Re: [AMBER] charmmlipid2amber.x error Ross Walker
- Re: [AMBER] strange CUDA benchmark Ross Walker
- Re: [AMBER] CUDA running error Ross Walker
- Re: [AMBER] error in SMD David A Case
- Re: [AMBER] strange CUDA benchmark Albert
- Re: [AMBER] charmmlipid2amber.x error Albert
- Re: [AMBER] strange CUDA benchmark Jason Swails
- Re: [AMBER] CUDA running error Albert
- Re: [AMBER] strange CUDA benchmark Albert
- Re: [AMBER] CUDA running error Ross Walker
- Re: [AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 ) c00jsw00.nchc.narl.org.tw
- Re: [AMBER] CUDA running error Albert
- Re: [AMBER] CUDA running error Ross Walker
- Re: [AMBER] CUDA running error Albert
- [AMBER] Zinc ion with five coordination bonds Jagur Lambix
- Re: [AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 ) Brian Radak
- Re: [AMBER] MCPB espgen error Robin Betz
- [AMBER] inconsistent results in MMPBSA w/o energy decomposition Victor Ma
- Re: [AMBER] inconsistent results in MMPBSA w/o energy decomposition Bill Miller III
- Re: [AMBER] charmmlipid2amber.x error Benjamin D Madej
- Re: [AMBER] inconsistent results in MMPBSA w/o energy decomposition Jason Swails
- Re: [AMBER] charmmlipid2amber.x error Albert
- [AMBER] Purchasing -challenged researcher seeks help on GPU purchase David Cowburn
- Re: [AMBER] inconsistent results in MMPBSA w/o energy decomposition Victor Ma
- Re: [AMBER] inconsistent results in MMPBSA w/o energy decomposition Victor Ma
- Re: [AMBER] inconsistent results in MMPBSA w/o energy decomposition Bill Miller III
- Re: [AMBER] Purchasing -challenged researcher seeks help on GPU purchase Ross Walker
- Re: [AMBER] charmmlipid2amber.x error Albert
- Re: [AMBER] charmmlipid2amber.x error Benjamin D Madej
- Re: [AMBER] charmmlipid2amber.x error Albert
- Re: [AMBER] non-polar solvation energies decomposed in PB Jason Swails
- Re: [AMBER] charmmlipid2amber.x error Benjamin D Madej
- [AMBER] Zinc ion with five coordination bonds Jagur Lambix
- Re: [AMBER] non-polar solvation energies decomposed in PB Qiong Zhang
- [AMBER] qmmmmask Jacopo Sgrignani
- Re: [AMBER] qmmmmask Ben Roberts
- [AMBER] remd simulation Nadeem Ahmad Vellore
- [AMBER] Sander Error Melissa Buskes
- Re: [AMBER] Sander Error Ben Roberts
- Re: [AMBER] PLEASE GIVE SOME SUGGESTION jit mukherjee
- Re: [AMBER] help with pmemd .in file Chris Chris
- Re: [AMBER] MMPBSA calculation of large proteins Jyotsna Bhat
- [AMBER] vdW parameters for cations Jesper Sørensen
- Re: [AMBER] error in SMD mehdi bagherpoor
- [AMBER] SA Bomb in sa_arc(): Allocation aborted jyoti alyan
Wednesday, 9 May 2012
- [AMBER] My email Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] PLEASE GIVE SOME SUGGESTION steinbrt.rci.rutgers.edu
- Re: [AMBER] charmmlipid2amber.x error Albert
- Re: [AMBER] charmmlipid2amber.x error Albert
- Re: [AMBER] charmmlipid2amber.x error Albert
- [AMBER] bug.7 for Amber 12 has some problem Albert
- Re: [AMBER] bug.7 for Amber 12 has some problem Jason Swails
- Re: [AMBER] Zinc ion with five coordination bonds FyD
- Re: [AMBER] charmmlipid2amber.x error David A Case
- Re: [AMBER] remd simulation Carlos Simmerling
- Re: [AMBER] remd simulation Daniel Roe
- Re: [AMBER] MCPB espgen error Fabrício Bracht
- Re: [AMBER] bug.7 for Amber 12 has some problem Albert
- [AMBER] how to specify CUDA devices? Albert
- Re: [AMBER] charmmlipid2amber.x error Albert
- Re: [AMBER] MMPBSA calculation of large proteins Bill Miller III
- Re: [AMBER] SA Bomb in sa_arc(): Allocation aborted Bill Miller III
- Re: [AMBER] how to specify CUDA devices? Jason Swails
- Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? Marek Maly
- Re: [AMBER] MMPBSA calculation of large proteins Jyotsna Bhat
- Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? steinbrt.rci.rutgers.edu
- [AMBER] Problems doing MD on protein complex Chris Chris
- Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? Marek Maly
- [AMBER] how much dyne/cm should we use for lipids? Albert
- [AMBER] Question on Entropy and MMPBSA calculation Kumar, Sonu
- Re: [AMBER] SA Bomb in sa_arc(): Allocation aborted Ray Luo, Ph.D.
- Re: [AMBER] MMPBSA calculation of large proteins Ray Luo
- [AMBER] Zinc ion with five coordination bonds Jagur Lambix
- [AMBER] different files for protein-protein complex? Asmita Gupta
- [AMBER] is NPAT available in Amber 12? Albert
- Re: [AMBER] vdW parameters for cations Jesper Sørensen
- Re: [AMBER] qmmmmask Brian Radak
- Re: [AMBER] Problems doing MD on protein complex Dean Cuebas
- Re: [AMBER] qmmmmask Jacopo Sgrignani
- [AMBER] job error Albert
- Re: [AMBER] Question on Entropy and MMPBSA calculation Jason Swails
- Re: [AMBER] job error Jason Swails
- Re: [AMBER] job error Albert
- Re: [AMBER] job error Jason Swails
- Re: [AMBER] job error Albert
- Re: [AMBER] job error Bill Ross
- [AMBER] MM-RISM and per residue energy decomposition Lucas A. Defelipe
- Re: [AMBER] job error David A Case
- Re: [AMBER] job error Bill Ross
- Re: [AMBER] MM-RISM and per residue energy decomposition Dwight McGee
- Re: [AMBER] Problems doing MD on protein complex Chris Chris
- [AMBER] Energy Differences between mmpbsa_py_energy and sander outputs (reposting) Damodaran, Komath
- [AMBER] question about cpptraj surf command Sidney Elmer
- Re: [AMBER] question about cpptraj surf command Daniel Roe
- Re: [AMBER] question about cpptraj surf command Sidney Elmer
- Re: [AMBER] job error Albert
Thursday, 10 May 2012
- [AMBER] how to assign SS bond? Albert
- Re: [AMBER] how to assign SS bond? Albert
- Re: [AMBER] job error Marc van der Kamp
- Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? steinbrt.rci.rutgers.edu
- Re: [AMBER] job error Albert
- Re: [AMBER] job error Albert
- [AMBER] Umbrella sampling mehdi bagherpoor
- [AMBER] AM1-DH+ marawan hussain
- Re: [AMBER] job error Marc van der Kamp
- [AMBER] Amber11 using openmpi (parallel install problem) yjzhao.wh.gmail.com
- Re: [AMBER] Amber11 using openmpi (parallel install problem) David A Case
- Re: [AMBER] MCPB espgen error Fabrício Bracht
- Re: [AMBER] question about cpptraj surf command Daniel Roe
- Re: [AMBER] Umbrella sampling ros
- [AMBER] Electrostatic potential calculation Sudarshan Debnath
- Re: [AMBER] Electrostatic potential calculation Ray Luo, Ph.D.
- Re: [AMBER] AM1-DH+ Andreas Goetz
- [AMBER] parameters for Zinc ion with five coordination bonds. Jagur Lambix
- [AMBER] how can we add ACE and NME to to the cap protein terminal? Albert
- [AMBER] Problem with the binding free energy from MMPBSA decomposed energies Qiong Zhang
- Re: [AMBER] how can we add ACE and NME to to the cap protein terminal? case
- Re: [AMBER] FW: getting metal ions coordinates of nmr structures of a protein Mahendra B Thapa
- Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? Marek Maly
- Re: [AMBER] parameters for Zinc ion with five coordination bonds. Ben Roberts
- Re: [AMBER] parameters for Zinc ion with five coordination bonds. Hector A. Baldoni
- Re: [AMBER] FW: getting metal ions coordinates of nmr structures of a protein Daniel Sindhikara
- [AMBER] How to generate single mismatch DNA duplex using NAB natty yoshisawa
- Re: [AMBER] how can we add ACE and NME to to the cap protein terminal? Albert
- Re: [AMBER] how can we add ACE and NME to to the cap protein terminal? tdo.chem.ucsb.edu
Friday, 11 May 2012
- [AMBER] regarding REMD Dilraj LAMA
- [AMBER] lipid11 problem with leap Tales Yuan
- [AMBER] lipid11 problem with leap Tales Yuan
- [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09
- [AMBER] slow AMBER on my machine Cao Yang
- [AMBER] lipid11 force filed problem with tleap Tales Yuan
- [AMBER] sander.MPI error George Tzotzos
- [AMBER] Difference in PB results of mmpbsa and mmpbsa.mpi amin.imtech.res.in
- [AMBER] does LIPID11 require surface tension ? Vlad Cojocaru
- [AMBER] lipid11 force filed question Tales Yuan
- [AMBER] Quantification of forces Soumya Lipsa Rath
- Re: [AMBER] Quantification of forces steinbrt.rci.rutgers.edu
- Re: [AMBER] how can we add ACE and NME to to the cap protein terminal? David A Case
- Re: [AMBER] Problem regarding antechamber David A Case
- Re: [AMBER] slow AMBER on my machine David A Case
- Re: [AMBER] Difference in PB results of mmpbsa and mmpbsa.mpi Bill Miller III
- Re: [AMBER] sander.MPI error Jason Swails
- Re: [AMBER] sander.MPI error George Tzotzos
- Re: [AMBER] lipid11 force filed question Jason Swails
- Re: [AMBER] sander.MPI error Jason Swails
- Re: [AMBER] lipid11 force filed question Tales Yuan
- Re: [AMBER] regarding REMD Jason Swails
- Re: [AMBER] lipid11 force filed question Jason Swails
- Re: [AMBER] sander.MPI error George Tzotzos
- Re: [AMBER] sander.MPI error Marc van der Kamp
- Re: [AMBER] sander.MPI error George Tzotzos
- Re: [AMBER] how can we add ACE and NME to to the cap protein terminal? Albert
- Re: [AMBER] lipid11 force filed question Albert
- Re: [AMBER] lipid11 force filed question Vlad Cojocaru
- Re: [AMBER] lipid11 force filed question Albert
- Re: [AMBER] regarding REMD Carlos Simmerling
- Re: [AMBER] Problem with the binding free energy from MMPBSA decomposed energies Qiong Zhang
- Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] lipid11 force filed question Ross Walker
- Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined tluchko
- Re: [AMBER] how can we add ACE and NME to to the cap protein terminal? Sajeewa Pemasinghe
- Re: [AMBER] Energy Differences between mmpbsa_py_energy and sander outputs (reposting) Bill Miller III
- Re: [AMBER] lipid11 force filed question Albert
- Re: [AMBER] lipid11 force filed question Tales Yuan
- Re: [AMBER] lipid11 force filed question Daniel Roe
- [AMBER] RNA xleap Charles Johnson
- Re: [AMBER] lipid11 force filed question Tales Yuan
- Re: [AMBER] lipid11 force filed question Ross Walker
- Re: [AMBER] lipid11 force filed question Ross Walker
- Re: [AMBER] lipid11 force filed question Ross Walker
- Re: [AMBER] lipid11 force filed question Gould, Ian R
- Re: [AMBER] lipid11 force filed question Ross Walker
- Re: [AMBER] lipid11 force filed question Albert
- Re: [AMBER] lipid11 force filed question Tales Yuan
- Re: [AMBER] regarding REMD David A Case
- Re: [AMBER] Problem regarding antechamber David A Case
- Re: [AMBER] RNA xleap David A Case
- Re: [AMBER] lipid11 force filed question Albert
- Re: [AMBER] regarding REMD Carlos Simmerling
- Re: [AMBER] how can we add ACE and NME to to the cap protein terminal? Albert
- Re: [AMBER] RNA xleap Charles Johnson
- Re: [AMBER] RNA xleap David A Case
- Re: [AMBER] lipid11 force filed question Benjamin D Madej
- Re: [AMBER] sander.MPI error Jason Swails
- Re: [AMBER] regarding REMD Jason Swails
- Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined Mark Rance
- Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined David A Case
- Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined Mark Rance
- Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined Jason Swails
- Re: [AMBER] am1d problem Gabriel Jara
- Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09
Saturday, 12 May 2012
- Re: [AMBER] am1d problem Andreas Goetz
- [AMBER] apply an external force mehdi bagherpoor
- Re: [AMBER] apply an external force ros
- Re: [AMBER] apply an external force case
- Re: [AMBER] How to generate single mismatch DNA duplex using NAB case
- [AMBER] Placing molecules randomly in a simulation box Massimiliano Porrini
- Re: [AMBER] How to generate single mismatch DNA duplex using NAB M. L. Dodson
- Re: [AMBER] Placing molecules randomly in a simulation box Lachele Foley (Lists)
- [AMBER] Large standard deviation of entropy obtained from NMODE Xioling Chuang
Sunday, 13 May 2012
- Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined Mark Rance
- Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined Jason Swails
- Re: [AMBER] How to generate single mismatch DNA duplex using NAB natty yoshisawa
- [AMBER] bi-layer membrane system shrink with NPgamaT Albert
Monday, 14 May 2012
- Re: [AMBER] bi-layer membrane system shrink with NPgamaT Åge Skjevik
- Re: [AMBER] bi-layer membrane system shrink with NPgamaT Albert
- [AMBER] qmmm_EXTERN/ tests failing Marc van der Kamp
- Re: [AMBER] Large standard deviation of entropy obtained from NMODE Jason Swails
- [AMBER] problems with added hydrogens to non standard residue Urszula Uciechowska
- [AMBER] printing out total energy in sander with high precision (more digits) Marc van der Kamp
- Re: [AMBER] printing out total energy in sander with high precision (more digits) Mark Williamson
- Re: [AMBER] printing out total energy in sander with high precision (more digits) Marc van der Kamp
- Re: [AMBER] Placing molecules randomly in a simulation box Dickson, Callum
- Re: [AMBER] printing out total energy in sander with high precision (more digits) Mark Williamson
- Re: [AMBER] problems with added hydrogens to non standard residue FyD
- [AMBER] Amber 12 parallel compilation error Fernando Martín García
- [AMBER] Not able to apply bugfix on Amber 11 HIMANSHU JOSHI
- Re: [AMBER] Amber 12 parallel compilation error Fernando Martín García
- Re: [AMBER] problems with added hydrogens to non standard residue Urszula Uciechowska
- Re: [AMBER] Placing molecules randomly in a simulation box Marek Maly
- Re: [AMBER] Placing molecules randomly in a simulation box Massimiliano Porrini
- Re: [AMBER] problems with added hydrogens to non standard residue Renata KWIECIEN
- Re: [AMBER] How to generate single mismatch DNA duplex using NAB Charles Johnson
- Re: [AMBER] Not able to apply bugfix on Amber 11 Jason Swails
- Re: [AMBER] printing out total energy in sander with high precision (more digits) Jason Swails
- Re: [AMBER] printing out total energy in sander with high precision (more digits) Marc van der Kamp
- [AMBER] ACPYPE error Albert
- Re: [AMBER] qmmm_EXTERN/ tests failing Jason Swails
- [AMBER] NetCDF Restart Files - Amber 12 Lucas A. Defelipe
- Re: [AMBER] NetCDF Restart Files - Amber 12 Jason Swails
- Re: [AMBER] ACPYPE error Alan
- Re: [AMBER] Not able to apply bugfix on Amber 11 HIMANSHU JOSHI
- [AMBER] problem installing AMBER12 on MacOSX Robert Oswald
- Re: [AMBER] problem installing AMBER12 on MacOSX Jason Swails
- Re: [AMBER] Not able to apply bugfix on Amber 11 Jason Swails
- Re: [AMBER] problem installing AMBER12 on MacOSX Robert Oswald
- Re: [AMBER] NetCDF Restart Files - Amber 12 Daniel Roe
- Re: [AMBER] problem installing AMBER12 on MacOSX Jason Swails
- [AMBER] Errrors in mm_pbsa.pl Souvik Sur
- [AMBER] How does radial work? Alan
- Re: [AMBER] qmmm_EXTERN/ tests failing Marc van der Kamp
- [AMBER] Periodicity errors in pymdsapb Genzo Tanaka
- Re: [AMBER] Periodicity errors in pymdsapb Genzo Tanaka
- Re: [AMBER] Errrors in mm_pbsa.pl Ray Luo, Ph.D.
- [AMBER] Bug? Zero decomposed vdw and ele energies for explicit water molecules in the decomposed PB calculation. Qiong Zhang
- Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined Mark Rance
- Re: [AMBER] qmmm_EXTERN/ tests failing Jason Swails
- Re: [AMBER] qmmm_EXTERN/ tests failing Andreas Goetz
- Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined tluchko
- Re: [AMBER] Periodicity errors in pymdsapb case
- [AMBER] Fwd: Bug? Zero decomposed vdw and ele energies for explicit water molecules in the decomposed PB calculation. Ray Luo, Ph.D.
- [AMBER] Antechamber Error Pedro Swagger
- Re: [AMBER] Antechamber Error case
- [AMBER] How to implement a new energy function in AMBER Xin Geng
- Re: [AMBER] How to implement a new energy function in AMBER Jason Swails
- Re: [AMBER] MCPB espgen error Robin Betz
- Re: [AMBER] How to implement a new energy function in AMBER Xin Geng
- Re: [AMBER] How to implement a new energy function in AMBER Jason Swails
- Re: [AMBER] Bug? Zero decomposed vdw and ele energies for explicit water molecules in the decomposed PB calculation. Qiong Zhang
- [AMBER] Build B form RNA by NAB? Hai Nguyen
- [AMBER] mpi problem Syed Tarique Moin
Tuesday, 15 May 2012
- Re: [AMBER] problems with added hydrogens to non standard residue FyD
- [AMBER] problem in reading pdb file Asmita Gupta
- Re: [AMBER] mpi problem Jason Swails
- Re: [AMBER] problem in reading pdb file case
- Re: [AMBER] qmmm_EXTERN/ tests failing Marc van der Kamp
- Re: [AMBER] problem in reading pdb file Asmita Gupta
- Re: [AMBER] qmmm_EXTERN/ tests failing Marc van der Kamp
- [AMBER] sleap/tleap differences for parmbsc0 DNA C.M. Baker
- Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] problem in reading pdb file case
- Re: [AMBER] mpi problem Syed Tarique Moin
- Re: [AMBER] sleap/tleap differences for parmbsc0 DNA case
- Re: [AMBER] problems with added hydrogens to non standard residue Urszula Uciechowska
- Re: [AMBER] Problem regarding antechamber case
- Re: [AMBER] problems with added hydrogens to non standard residue case
- Re: [AMBER] problems with added hydrogens to non standard residue Urszula Uciechowska
- Re: [AMBER] problems with added hydrogens to non standard residue FyD
- Re: [AMBER] problems with added hydrogens to non standard residue Urszula Uciechowska
- Re: [AMBER] mpi problem Jason Swails
- Re: [AMBER] Periodicity errors in pymdsapb Genzo Tanaka
- Re: [AMBER] Periodicity errors in pymdsapb Jason Swails
- Re: [AMBER] MCPB espgen error Fabrício Bracht
- Re: [AMBER] problem in reading pdb file Claire Shoemake
- [AMBER] MMPBSA.py problem marawan hussain
- Re: [AMBER] MMPBSA.py problem Bill Miller III
- Re: [AMBER] Large standard deviation of entropy obtained from NMODE Xioling Chuang
- Re: [AMBER] MMPBSA.py problem Jason Swails
- Re: [AMBER] MMPBSA.py problem marawan hussain
- Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] MMPBSA.py problem marawan hussain
- Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] mpi problem Syed Tarique Moin
- Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] MMPBSA.py problem case
- Re: [AMBER] Problem regarding antechamber case
- Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09
Wednesday, 16 May 2012
- [AMBER] Amber 12 cuda test failed Fernando Martín García
- Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] Problem regarding antechamber FyD
- Re: [AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 ) Yeng-Tseng Wang
- [AMBER] Electrostatic potential calculation. Sudarshan Debnath
- [AMBER] Several types of extra point charges in sander? Олег Титов
- [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large Urszula Uciechowska
- [AMBER] 1-4 scale factors Urszula Uciechowska
- [AMBER] charge and ionization state at pH 6.5 Acoot Brett
- Re: [AMBER] sleap/tleap differences for parmbsc0 DNA C.M. Baker
- [AMBER] Is the performance issue of CUDA 4.1 compilers resolved in CUDA 4.2 compilers? Jan-Philip Gehrcke
- Re: [AMBER] Is the performance issue of CUDA 4.1 compilers resolved in CUDA 4.2 compilers? filip fratev
- Re: [AMBER] problems with added hydrogens to non standard residue FyD
- Re: [AMBER] Is the performance issue of CUDA 4.1 compilers resolved in CUDA 4.2 compilers? Ross Walker
- Re: [AMBER] Amber 12 cuda test failed Ross Walker
- Re: [AMBER] Is the performance issue of CUDA 4.1 compilers resolved in CUDA 4.2 compilers? Scott Le Grand
- Re: [AMBER] How to implement a new energy function in AMBER Xin Geng
- Re: [AMBER] 1-4 scale factors Lachele Foley (Lists)
- Re: [AMBER] (no subject) DEBOSTUTI GHOSHDASTIDAR
- Re: [AMBER] Fwd: Bug? Zero decomposed vdw and ele energies for explicit water molecules in the decomposed PB calculation. Qin Cai
- [AMBER] new Mg parameters Asmita Gupta
- Re: [AMBER] new Mg parameters Jesper Sørensen
- Re: [AMBER] new Mg parameters Thomas Cheatham III
- Re: [AMBER] new Mg parameters Jesper Sørensen
- Re: [AMBER] 1-4 scale factors FyD
- Re: [AMBER] 1-4 scale factors Urszula Uciechowska
- Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large case
- Re: [AMBER] charge and ionization state at pH 6.5 case
- Re: [AMBER] 1-4 scale factors Lachele Foley (Lists)
- Re: [AMBER] mbondi3 Jesper Sørensen
- Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large Hai Nguyen
- Re: [AMBER] charge and ionization state at pH 6.5 Marek Maly
- Re: [AMBER] am1d problem Gabriel Jara
- Re: [AMBER] (no subject) case
- [AMBER] Electrostatic potential calculation Sudarshan Debnath
- Re: [AMBER] 1-4 scale factors Urszula Uciechowska
- Re: [AMBER] 1-4 scale factors FyD
- Re: [AMBER] Amber 12 cuda test failed Fernando Martín García
Thursday, 17 May 2012
- [AMBER] how to calculate the volume of our system? Albert
- [AMBER] cpptraj-secstruct colvin
- Re: [AMBER] cpptraj-secstruct Daniel Roe
- Re: [AMBER] 1-4 scale factors Urszula Uciechowska
- [AMBER] Force.dat file from pbsa calculation tommaso.casalini.mail.polimi.it
- Re: [AMBER] how to calculate the volume of our system? David A Case
- Re: [AMBER] how to calculate the volume of our system? Albert
- [AMBER] Electrostatic potential calculation Sudarshan Debnath
- Re: [AMBER] Periodicity errors in pymdsapb Genzo Tanaka
- [AMBER] Failure in mol surf in pymdpbsa Genzo Tanaka
- Re: [AMBER] Electrostatic potential calculation Ray Luo, Ph.D.
- Re: [AMBER] Electrostatic potential calculation Ray Luo, Ph.D.
- [AMBER] Iron-Sulfur Cluster Wilson, Katie
- Re: [AMBER] new Mg parameters Jiri Sponer
- Re: [AMBER] 1-4 scale factors Lachele Foley (Lists)
- Re: [AMBER] new Mg parameters Jesper Sørensen
- Re: [AMBER] new Mg parameters Jiri Sponer
- Re: [AMBER] Iron-Sulfur Cluster francesco oteri
- Re: [AMBER] How to implement a new energy function in AMBER Xin Geng
- [AMBER] prmtop generated from chamber colvin
- [AMBER] Electrostatic potential calculation Sudarshan Debnath
Friday, 18 May 2012
- Re: [AMBER] mpi problem Syed Tarique Moin
- Re: [AMBER] prmtop generated from chamber Marc van der Kamp
- [AMBER] The QMMM_MD err calculation of amber12+ gamessUS javacfish
- Re: [AMBER] new Mg parameters Asmita Gupta
- Re: [AMBER] new Mg parameters Jiri Sponer
- [AMBER] Electrostatic potential calculation Sudarshan Debnath
- [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI) Åge Skjevik
- Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI) Bill Miller III
- Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI) Åge Skjevik
- [AMBER] High Electrostatic Interaction Khaled Barakat
- Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI) Bill Miller III
- Re: [AMBER] Electrostatic potential calculation Ray Luo, Ph.D.
- Re: [AMBER] new Mg parameters Jesper Sørensen
- Re: [AMBER] prmtop generated from chamber Ross Walker
- Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI) Åge Skjevik
- Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI) Bill Miller III
- [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang
- Re: [AMBER] new Mg parameters Asmita Gupta
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Bill Miller III
- Re: [AMBER] Periodicity errors in pymdsapb Bill Miller III
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang
- [AMBER] was the bug fixed for tleap? Albert
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Bill Miller III
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Bill Miller III
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang
- [AMBER] Electrostatic potential calculation Sudarshan Debnath
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Bill Miller III
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang
- Re: [AMBER] Electrostatic potential calculation David A Case
- [AMBER] pmemd.cuda for JAC benchmark Mohammad Ashraf Bhuiyan
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Bill Miller III
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang
- Re: [AMBER] was the bug fixed for tleap? Benjamin D Madej
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Bill Miller III
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang
- [AMBER] Electrostatic potential calculation Sudarshan Debnath
- [AMBER] Electrostatic potential calculation Sudarshan Debnath
- Re: [AMBER] 1-4 scale factors FyD
Saturday, 19 May 2012
- Re: [AMBER] (no subject) DEBOSTUTI GHOSHDASTIDAR
- Re: [AMBER] Electrostatic potential calculation Jan-Philip Gehrcke
- Re: [AMBER] (no subject) case
- Re: [AMBER] (no subject) case
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Bill Miller III
- Re: [AMBER] MCPB espgen error Fabrício Bracht
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang
- Re: [AMBER] MCPB espgen error FyD
- Re: [AMBER] Build B form RNA by NAB? Hai Nguyen
- Re: [AMBER] Build B form RNA by NAB? Vlad Cojocaru
- Re: [AMBER] pmemd.cuda for JAC benchmark case
- Re: [AMBER] (no subject) DEBOSTUTI GHOSHDASTIDAR
- Re: [AMBER] (no subject) DEBOSTUTI GHOSHDASTIDAR
- [AMBER] Problem Installing Amber on Mac OSX Lion Arthur Roberts
Sunday, 20 May 2012
- [AMBER] Electrostatic potential calculation Sudarshan Debnath
- Re: [AMBER] Problem Installing Amber on Mac OSX Lion case
- Re: [AMBER] Build B form RNA by NAB? Hai Nguyen
- Re: [AMBER] Several types of extra point charges in sander? Jason Swails
- Re: [AMBER] sleap/tleap differences for parmbsc0 DNA Jason Swails
- Re: [AMBER] mbondi3 Jason Swails
- Re: [AMBER] Problem Installing Amber on Mac OSX Lion (lenin) Julio Dominguez
- Re: [AMBER] Problem Installing Amber on Mac OSX Lion Arthur Roberts
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Jason Swails
- Re: [AMBER] Problem Installing Amber on Mac OSX Lion Jason Swails
- [AMBER] MMPBSA-CalcError marawan hussain
- Re: [AMBER] MMPBSA-CalcError Bill Miller III
- Re: [AMBER] Problem Installing Amber on Mac OSX Lion Arthur Roberts
- Re: [AMBER] MMPBSA-CalcError marawan hussain
- Re: [AMBER] MMPBSA-CalcError Bill Miller III
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang
Monday, 21 May 2012
- Re: [AMBER] 1-4 scale factors Karl N. Kirschner
- [AMBER] Electrostatic potential calculation Sudarshan Debnath
- Re: [AMBER] lipid11 force filed question Daniel Roe
- Re: [AMBER] Electrostatic potential calculation Jan-Philip Gehrcke
- [AMBER] setting gcc compiler Alan
- [AMBER] Amber tools 12 and esp visualization in VMD and PyMol Sudarshan Debnath
- Re: [AMBER] lipid11 force filed question Ross Walker
- [AMBER] add new functions into Amber10 Xin Geng
- [AMBER] amber99tor and amber99ez force field Indrajit Deb
- Re: [AMBER] Electrostatic potential calculation Qin Cai
- Re: [AMBER] amber99tor and amber99ez force field David Condon
- Re: [AMBER] amber99tor and amber99ez force field Indrajit Deb
- Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI) Åge Skjevik
- Re: [AMBER] amber99tor and amber99ez force field David Condon
- Re: [AMBER] amber99tor and amber99ez force field Indrajit Deb
- Re: [AMBER] amber99tor and amber99ez force field Indrajit Deb
- Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI) Bill Miller III
- Re: [AMBER] lipid11 force filed question Daniel Roe
- Re: [AMBER] amber99tor and amber99ez force field David Condon
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang
- Re: [AMBER] Amber tools 12 and esp visualization in VMD and PyMol Ray Luo, Ph.D.
- Re: [AMBER] setting gcc compiler David A. Case
- [AMBER] OT -- Have a Model Setup Wish List? Lachele Foley (Lists)
- Re: [AMBER] add new functions into Amber10 David A. Case
- [AMBER] antechamber problem anyiphysics.gmail.com
- Re: [AMBER] antechamber problem Bill Ross
- Re: [AMBER] amber99tor and amber99ez force field Indrajit Deb
Tuesday, 22 May 2012
- Re: [AMBER] setting gcc compiler Alan
- Re: [AMBER] Visualizing ptraj eigenvectors steinbrt.rci.rutgers.edu
- Re: [AMBER] antechamber problem David A. Case
- [AMBER] where's http://ambermd.org/bugfixes/11.0/bugfix.all? Alan
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang
- [AMBER] High Electrostatic interaction Khaled Barakat
- [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster Qiong Zhang
- Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster Jan-Philip Gehrcke
- Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster Qiong Zhang
- Re: [AMBER] Periodicity errors in pymdsapb Genzo Tanaka
- Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster Jan-Philip Gehrcke
- Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster Qiong Zhang
- Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster Jan-Philip Gehrcke
- Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster Qiong Zhang
- [AMBER] cuda.a(kNLRadixSort. o): undefined reference to symbol '__cxa_pure_virtual Mark Rance
- [AMBER] refc error with PMEMD.MPI g t
- [AMBER] creating a primitive object such as a cylinder in amber g t
- Re: [AMBER] cpptraj-secstruct Daniel Roe
- [AMBER] Failure in mol surf in pymdpbsa Genzo Tanaka
- [AMBER] MM-PBSA ATP binding Alejandro Blanco
- [AMBER] ammonia parameters Sajeewa Pemasinghe
- Re: [AMBER] where's http://ambermd.org/bugfixes/11.0/bugfix.all? David A. Case
- Re: [AMBER] refc error with PMEMD.MPI David A. Case
- Re: [AMBER] MM-PBSA ATP binding Bill Miller III
- [AMBER] MMPBSA.py issues marawan hussain
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Bill Miller III
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang
- [AMBER] simulation with special amino acid yjzhao.wh.gmail.com
- [AMBER] High Electrostatic Energy in MMPBSA analysis Khaled Barakat
- [AMBER] Amber tools 12 and esp visualization in VMD and PyMol Sudarshan Debnath
Wednesday, 23 May 2012
- [AMBER] how can i introduce Zn2+ in amber Sanjib Paul
- Re: [AMBER] was the bug fixed for tleap? Albert
- [AMBER] convert error Albert
- Re: [AMBER] cpptraj-secstruct colvin
- Re: [AMBER] cpptraj-secstruct Marc van der Kamp
- Re: [AMBER] where's http://ambermd.org/bugfixes/11.0/bugfix.all? Alan
- [AMBER] how to introduce Zn2+ in amber Sanjib Paul
- Re: [AMBER] cpptraj-secstruct colvin
- Re: [AMBER] how to introduce Zn2+ in amber Marc van der Kamp
- Re: [AMBER] how to introduce Zn2+ in amber Urszula Uciechowska
- [AMBER] periodic box blow up kamlesh sahu
- Re: [AMBER] 1-4 scale factors Jason Swails
- Re: [AMBER] MMPBSA.py issues Jason Swails
- Re: [AMBER] MMPBSA.py issues David A. Case
- Re: [AMBER] simulation with special amino acid David A. Case
- Re: [AMBER] how can i introduce Zn2+ in amber David A. Case
- Re: [AMBER] periodic box blow up David A. Case
- Re: [AMBER] was the bug fixed for tleap? Åge Skjevik
- Re: [AMBER] simulation with special amino acid Yunjie Zhao
- [AMBER] Amber tools 12 and esp visualization in VMD and PyMol Sudarshan Debnath
- [AMBER] openf90 seg-faults during compilation Fluder, Eugene
- [AMBER] Amber tools 12 and esp visualization in VMD and PyMol Sudarshan Debnath
- [AMBER] DNA capping Mithun Biswas
- Re: [AMBER] Amber tools 12 and esp visualization in VMD and PyMol Jan-Philip Gehrcke
- Re: [AMBER] Visualisation of periodic boundary conditions within VMD Ben Ahmady
- Re: [AMBER] refc error with PMEMD.MPI g t
- Re: [AMBER] High Electrostatic Energy in MMPBSA analysis Ray Luo, Ph.D.
- Re: [AMBER] Amber tools 12 and esp visualization in VMD and PyMol Ray Luo, Ph.D.
- Re: [AMBER] Amber tools 12 and esp visualization in VMD and PyMol Ray Luo, Ph.D.
- Re: [AMBER] problem installing AMBER12 on MacOSX Philip Winter
- Re: [AMBER] The QMMM_MD err calculation of amber12+ gamessUS Andreas Goetz
- [AMBER] Antechamber Atom Types Sarah Edwards
- Re: [AMBER] mbondi3 Jesper Sørensen
- Re: [AMBER] mbondi3 Jason Swails
- Re: [AMBER] Antechamber Atom Types David A. Case
- Re: [AMBER] mbondi3 David A. Case
Monday, 21 May 2012
- [AMBER] problem with mol2 to pdb conversion Chris Chris
Wednesday, 23 May 2012
- [AMBER] Hydrogen bond energy calculation Aditya Padhi
- Re: [AMBER] AMBER Digest, Vol 162, Issue 3 jit mukherjee
- Re: [AMBER] how to introduce Zn2+ in amber Sanjib Paul
- [AMBER] SIMMULATION OF CARBON NANOTUBE jit mukherjee
- [AMBER] Problem in Amber11 Compilation HIMANSHU JOSHI
- [AMBER] Amber tools 12 and esp visualization in VMD and PyMol Sudarshan Debnath
- Re: [AMBER] periodic box blow up kamlesh sahu
Thursday, 24 May 2012
- [AMBER] Solvation of surfactant molecules Debolina Mitra
- Re: [AMBER] problem with mol2 to pdb conversion g t
- [AMBER] Generate Gaussian file in antechamber Debolina Mitra
- [AMBER] Amber tools 12 and esp visualization in VMD and PyMol Sudarshan Debnath
- [AMBER] Amber tools 12 and esp visualization in VMD and PyMol Sudarshan Debnath
- Re: [AMBER] problem with mol2 to pdb conversion Marc van der Kamp
- Re: [AMBER] problem installing AMBER12 on MacOSX David A Case
- Re: [AMBER] Problem in Amber11 Compilation David A Case
- Re: [AMBER] problem with mol2 to pdb conversion George Tzotzos
- [AMBER] Electrostatic potential and forces computation tommaso.casalini.mail.polimi.it
- Re: [AMBER] AMBER Digest, Vol 162, Issue 3 Julio Dominguez
- Re: [AMBER] Electrostatic potential and forces computation Ray Luo, Ph.D.
- Re: [AMBER] Electrostatic potential and forces computation Qin Cai
- [AMBER] large deviation on entropy value using ambertools1.5 manikanthan bhavaraju
- Re: [AMBER] SIMMULATION OF CARBON NANOTUBE FyD
- Re: [AMBER] DNA capping FyD
- Re: [AMBER] Solvation of surfactant molecules FyD
- Re: [AMBER] SIMMULATION OF CARBON NANOTUBE Markus Kaukonen
Friday, 25 May 2012
- [AMBER] Reallocation of memory space Debolina Mitra
- [AMBER] AM1/D - ATP+PROTEIN Fernando Martín García
- [AMBER] Problem regarding CaDA Sanjib Paul
- Re: [AMBER] Problem regarding CaDA Marc van der Kamp
- [AMBER] manual prmtop file editing for free energy calculation Audrius Laurynėnas
- Re: [AMBER] DNA capping David A Case
- [AMBER] input card for relative permittivity Bala subramanian
- Re: [AMBER] AM1/D - ATP+PROTEIN Brian Radak
- Re: [AMBER] manual prmtop file editing for free energy calculation Brian Radak
- Re: [AMBER] AM1/D - ATP+PROTEIN Fernando Martín García
- Re: [AMBER] Iron-Sulfur Cluster Wilson, Katie
- Re: [AMBER] Electrostatic potential and forces computation tommaso.casalini.mail.polimi.it
- Re: [AMBER] Iron-Sulfur Cluster francesco oteri
- [AMBER] Fwd: Electrostatic potential and forces computation Ray Luo, Ph.D.
- Re: [AMBER] SIMMULATION OF CARBON NANOTUBE jit mukherjee
- [AMBER] pnetcdf.h missing in compiling of ptraj.MPI Yubo Fan
- [AMBER] Two Dimensional Periodic Boundary Conditions Zubin Kuvadia
- [AMBER] How can we make sure we have the extent of conformational sampling is enough? Catein Catherine
- [AMBER] How to calculate entropy lost upon binding? Catein Catherine
- Re: [AMBER] problem installing AMBER12 on MacOSX Jason Swails
- Re: [AMBER] pnetcdf.h missing in compiling of ptraj.MPI Jason Swails
- Re: [AMBER] problem installing AMBER12 on MacOSX David Watson
Saturday, 26 May 2012
- [AMBER] Saving the original position of atoms on using LEaP Francesco Pietra
- [AMBER] Can AMBER do Go model? Catein Catherine
- [AMBER] large deviation on entropy value using ambertools1.5 manikanthan bhavaraju
- Re: [AMBER] Electrostatic potential and forces computation Qin Cai
- [AMBER] relaxation time kirtana S
Sunday, 27 May 2012
- [AMBER] Problem regarding CaDA Sanjib Paul
Saturday, 26 May 2012
- Re: [AMBER] manual prmtop file editing for free energy calculation Jason Swails
Sunday, 27 May 2012
- Re: [AMBER] Electrostatic potential and forces computation Ray Luo, Ph.D.
- Re: [AMBER] Saving the original position of atoms on using LEaP case
- Re: [AMBER] relaxation time Jason Swails
- [AMBER] why is internal energy not taken into account for G gas? Xioling Chuang
- [AMBER] How to get a reliable RMSF value? aa aa
- Re: [AMBER] Help! Assigned Bond types are wrong ashley chen
Monday, 28 May 2012
- Re: [AMBER] Help! Assigned Bond types are wrong Marc van der Kamp
- [AMBER] conformational entropy of a peptide - how to calculate with AMBER? aa aa
- Re: [AMBER] why is internal energy not taken into account for G gas? Bill Miller III
- Re: [AMBER] Help! Assigned Bond types are wrong case
- Re: [AMBER] large deviation on entropy value using ambertools1.5 Bill Miller III
- [AMBER] Compile Amber 12 with IBM compilers Yubo Fan
- [AMBER] How to resume production phase simulation from power failure? bin wang
- [AMBER] Volume fraction John S
- Re: [AMBER] Compile Amber 12 with IBM compilers case
- Re: [AMBER] How to resume production phase simulation from power failure? case
- Re: [AMBER] why is internal energy not taken into account for G gas? Jason Swails
- Re: [AMBER] AMBER Digest, Vol 162, Issue 3 Jason Swails
- Re: [AMBER] Compile Amber 12 with IBM compilers Yubo Fan
- Re: [AMBER] Help! Assigned Bond types may be wrong ashley chen
- [AMBER] simmulation of carbon nanotube jit mukherjee
- [AMBER] Reallocation of memory space Debolina Mitra
- Re: [AMBER] large deviation on entropy value using ambertools1.5 Cao Yang
Tuesday, 29 May 2012
- [AMBER] Looping over a trajectory Lee-Ping Wang
- Re: [AMBER] Electrostatic potential and forces computation tommaso.casalini.mail.polimi.it
- [AMBER] Can I use “-rewrite-output” option in redoing the free energy calculation Cao Yang
- Re: [AMBER] Compile Amber 12 with IBM compilers David A Case
- Re: [AMBER] Help! Assigned Bond types may be wrong David A Case
- Re: [AMBER] Can I use “-rewrite-output” option in redoing the free energy calculation Bill Miller III
- Re: [AMBER] Looping over a trajectory David A Case
- [AMBER] High standard deviation in entropy and decomping calculation Cao Yang
- Re: [AMBER] High standard deviation in entropy and decomping calculation Bill Miller III
- Re: [AMBER] How to resume production phase simulation from power failure? bin wang
- Re: [AMBER] large deviation on entropy value using ambertools1.5 Jason Swails
- Re: [AMBER] How to get a reliable RMSF value? Jason Swails
- Re: [AMBER] Visualisation of periodic boundary conditions within VMD Jason Swails
- Re: [AMBER] Can I use “-rewrite-output” option in redoing the free energy calculation Jason Swails
- Re: [AMBER] large deviation on entropy value using ambertools1.5 Jason Swails
- Re: [AMBER] Looping over a trajectory Lee-Ping Wang
- Re: [AMBER] Looping over a trajectory Jason Swails
- Re: [AMBER] High standard deviation in entropy and decomping calculation Jason Swails
- Re: [AMBER] Looping over a trajectory Lee-Ping Wang
- Re: [AMBER] Looping over a trajectory Jason Swails
- Re: [AMBER] Looping over a trajectory Lee-Ping Wang
- Re: [AMBER] Looping over a trajectory Jason Swails
- [AMBER] multi-threading cpu's or no multi-threading Jonathan Gough
- Re: [AMBER] multi-threading cpu's or no multi-threading Jason Swails
- Re: [AMBER] why is internal energy not taken into account for G gas? Xioling Chuang
- Re: [AMBER] large deviation on entropy value using ambertools1.5 Cao Yang
- Re: [AMBER] multi-threading cpu's or no multi-threading Jonathan Gough
- Re: [AMBER] multi-threading cpu's or no multi-threading Jason Swails
- Re: [AMBER] large deviation on entropy value using ambertools1.5 Jason Swails
- Re: [AMBER] large deviation on entropy value using ambertools1.5 Cao Yang
- Re: [AMBER] MCPB espgen error Fabrício Bracht
- Re: [AMBER] large deviation on entropy value using ambertools1.5 Jason Swails
- Re: [AMBER] large deviation on entropy value using ambertools1.5 Cao Yang
- Re: [AMBER] large deviation on entropy value using ambertools1.5 Jason Swails
- Re: [AMBER] MCPB espgen error FyD
Wednesday, 30 May 2012
- [AMBER] Problem regarding simulation of bio-molecules using AMBER 9 somedatta pal
- Re: [AMBER] Problem regarding simulation of bio-molecules using AMBER 9 David A Case
- Re: [AMBER] large deviation on entropy value using ambertools1.5 Cao Yang
- [AMBER] Trouble compiling cuda, need help. Jonathan Gough
- Re: [AMBER] large deviation on entropy value using ambertools1.5 Jason Swails
- [AMBER] problem with solute that breaks up Massimiliano Porrini
- [AMBER] Amber 12 on x86_64 CentOS 5 Kevin Parkes
- Re: [AMBER] Amber 12 on x86_64 CentOS 5 Jason Swails
- Re: [AMBER] Trouble compiling cuda, need help. Jason Swails
- Re: [AMBER] Trouble compiling cuda, need help. Jonathan Gough
- Re: [AMBER] Amber 12 on x86_64 CentOS 5 Kevin Parkes
- Re: [AMBER] problem with solute that breaks up David A Case
- Re: [AMBER] Amber 12 on x86_64 CentOS 5 Jason Swails
- Re: [AMBER] Trouble compiling cuda, need help. Ross Walker
- Re: [AMBER] Trouble compiling cuda, need help. Jonathan Gough
- Re: [AMBER] Trouble compiling cuda, need help. Ross Walker
- Re: [AMBER] Trouble compiling cuda, need help. Jonathan Gough
- Re: [AMBER] problem with solute that breaks up Massimiliano Porrini
- Re: [AMBER] Trouble compiling cuda, need help. David A Case
- Re: [AMBER] Trouble compiling cuda, need help. Jonathan Gough
- Re: [AMBER] Trouble compiling cuda, need help. Jonathan Gough
- Re: [AMBER] Trouble compiling cuda, need help. Ross Walker
- Re: [AMBER] Trouble compiling cuda, need help. Jonathan Gough
- [AMBER] how long does cuda test usually take? Jonathan Gough
- Re: [AMBER] how long does cuda test usually take? Jason Swails
- Re: [AMBER] how long does cuda test usually take? Jonathan Gough
- Re: [AMBER] how long does cuda test usually take? Scott Le Grand
- Re: [AMBER] problem with solute that breaks up Jason Swails
- Re: [AMBER] problem with solute that breaks up Thomas Cheatham
- Re: [AMBER] Trouble compiling cuda, need help. Scott Le Grand
- [AMBER] Heme force field hwchem chem
- Re: [AMBER] how long does cuda test usually take? Jonathan Gough
- Re: [AMBER] am1d problem Brian Radak
- Re: [AMBER] Trouble compiling cuda, need help. case
- [AMBER] How AMBER process the energy of hydrogen bond Acoot Brett
Thursday, 31 May 2012
- [AMBER] Cuda-enabled amber 11 installation error Rajeswari A.
- [AMBER] Loading charged Peptide in tleap Thorsten Pisternick
- Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] Problem regarding antechamber FyD
- Re: [AMBER] Heme force field Mark Williamson
- Re: [AMBER] Loading charged Peptide in tleap case
- Re: [AMBER] How AMBER process the energy of hydrogen bond Brian Radak
- Re: [AMBER] Cuda-enabled amber 11 installation error case
- [AMBER] ptraj Hbond analysis shradhey gupta
- Re: [AMBER] problem with solute that breaks up Massimiliano Porrini
- Re: [AMBER] Amber 12 on x86_64 CentOS 5 Kevin Parkes
- Re: [AMBER] Cuda-enabled amber 11 installation error Rajeswari A.
- [AMBER] ptraj Hbond analysis shradhey gupta
- [AMBER] ptraj Hbond analysis shradhey gupta
- [AMBER] ptraj Hbond analysis shradhey gupta
- [AMBER] mm_pbsa.pl analysis bmartini
- Re: [AMBER] MCPB espgen error Fabrício Bracht
- Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Bill Miller III
- [AMBER] Ptraj and new netcdf Restart files Joshua Adelman
- [AMBER] base pairs missing from nastruct analysis of canonical B-DNA dodecamer Dean Cuebas
- Re: [AMBER] Ptraj and new netcdf Restart files Jason Swails
- Re: [AMBER] MCPB espgen error FyD
- Re: [AMBER] Problem Installing Amber on Mac OSX Lion Jason Swails
- Re: [AMBER] Problem Installing Amber on Mac OSX Lion Jason Swails
- [AMBER] problem with running equilibration MD in an LES system Sajeewa Pemasinghe
- Re: [AMBER] base pairs missing from nastruct analysis of canonical B-DNA dodecamer Daniel Roe
- [AMBER] Fwd: problem with running equilibration MD in an LES system Sajeewa Pemasinghe
- Re: [AMBER] Heme force field Yue
- Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Bill Miller III
- Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Jason Swails
- [AMBER] Trouble calculating free energy bmartini
- Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Jason Swails
- Re: [AMBER] cuda errors Ross Walker

Last message date: Thu May 31 2012 - 22:00:02 PDT
Archived on: Fri Apr 26 2024 - 05:54:38 PDT

Amber Archive May 2012 by date