Amber Archive May 2014: by date

Wednesday, 30 April 2014
- Re: [AMBER] How to extract each frame of a trajectory as individual .mdcrd files? Yew Mun Yip
Thursday, 1 May 2014
- [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 James Starlight
- Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight
- Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 David A Case
- Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Jason Swails
- [AMBER] Parameters for FAD amin.imtech.res.in
- Re: [AMBER] Parameters for FAD ABEL Stephane 175950
- Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 James Starlight
- Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 David A Case
- Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 James Starlight
- Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 Daniel Roe
- Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 James Starlight
- Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 James Starlight
- Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 Jason Swails
- Re: [AMBER] Parameters for FAD amin.imtech.res.in
- Re: [AMBER] Parameters for FAD Jason Swails
- [AMBER] solvating molecule kirtana S
- Re: [AMBER] Parameters for FAD amin.imtech.res.in
- [AMBER] Prepareing branched residue kurisaki
- Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Josh Berryman
- Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Josh Berryman
Friday, 2 May 2014
- Re: [AMBER] Parameters for FAD Jason Swails
- [AMBER] Intermittent error during T-REMD on 8 GPU computer Milo Westler
- Re: [AMBER] Intermittent error during T-REMD on 8 GPU computer Jason Swails
- [AMBER] Percent Occupancey with PCA Nicole Ippolito
- Re: [AMBER] Intermittent error during T-REMD on 8 GPU computer Milo Westler
Saturday, 3 May 2014
- Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 James Starlight
- Re: [AMBER] Percent Occupancey with PCA Daniel Roe
- [AMBER] alanine scanning Nitin Sharma
- Re: [AMBER] alanine scanning Bill Miller III
- [AMBER] vlimit exceeded error when switch from NPT to NVE Quynh Vo
- [AMBER] sander? sammia khatak
Sunday, 4 May 2014
- [AMBER] Questions about nmode Command 张明焜
- Re: [AMBER] vlimit exceeded error when switch from NPT to NVE David A Case
- Re: [AMBER] Questions about nmode Command David A Case
- Re: [AMBER] sander? David A Case
- Re: [AMBER] alanine scanning Nitin Sharma
- Re: [AMBER] vlimit exceeded error when switch from NPT to NVE Quynh Vo
- [AMBER] Fwd: Re: [q4md-fft] FAD parameters from F-90 FyD
- Re: [AMBER] how to protonate phosphate groups of nucleotides FyD
- Re: [AMBER] Prepareing branched residue FyD
Monday, 5 May 2014
- [AMBER] acpype on ambertools13 Ahmet yıldırım
- [AMBER] psf generation sammia khatak
- Re: [AMBER] psf generation Soumendranath Bhakat
- Re: [AMBER] psf generation Jason Swails
- Re: [AMBER] acpype on ambertools13 Jason Swails
- Re: [AMBER] acpype on ambertools13 Ahmet yıldırım
- [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED FyD
- Re: [AMBER] acpype on ambertools13 Jason Swails
- Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED Marek Maly
- Re: [AMBER] Extract velocity from the restart file Yin, Guowei
- Re: [AMBER] Extract velocity from the restart file Jason Swails
- Re: [AMBER] Extract velocity from the restart file Yin, Guowei
- [AMBER] Extract MD co-ordinates Soumendranath Bhakat
- [AMBER] Installation of AmberTools13 fabien.ibanez.modis.fr.netgrs.com
- Re: [AMBER] acpype on ambertools13 Alan
- [AMBER] Percent Occupancy with PCA Nicole Ippolito
- Re: [AMBER] Percent Occupancey with PCA Nicole Ippolito
- Re: [AMBER] Installation of AmberTools13 Jason Swails
- Re: [AMBER] Percent Occupancy with PCA Jason Swails
- Re: [AMBER] Extract MD co-ordinates Daniel Roe
- Re: [AMBER] Extract MD co-ordinates Soumendranath Bhakat
- Re: [AMBER] Extract MD co-ordinates Jason Swails
- [AMBER] PMF as a function of Q, fraction of native contacts Nihal Korkmaz
- [AMBER] handling long trajs for PCA and components plot newamber list
- Re: [AMBER] PMF as a function of Q, fraction of native contacts Carlos Simmerling
- Re: [AMBER] handling long trajs for PCA and components plot David A Case
- Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED FyD
- [AMBER] Regarding Calculation of Hydrogen Bond Energy MOHD HOMAIDUR RAHMAN
Tuesday, 6 May 2014
- [AMBER] Problem with the amber-14 compilation on Debian James Starlight
- [AMBER] Pairwise interaction energy between each residue MOHD HOMAIDUR RAHMAN
- [AMBER] Membrane protein simulation James Starlight
- Re: [AMBER] Membrane protein simulation Jason Swails
- Re: [AMBER] Problem with the amber-14 compilation on Debian Jason Swails
- [AMBER] number of frames in MMPBGBSA Nitin Sharma
- Re: [AMBER] PMF as a function of Q, fraction of native contacts Brian Radak
- Re: [AMBER] PMF as a function of Q, fraction of native contacts Adrian Roitberg
- Re: [AMBER] Problem with the amber-14 compilation on Debian James Starlight
- Re: [AMBER] Pairwise interaction energy between each residue Jason Swails
- Re: [AMBER] number of frames in MMPBGBSA Bill Miller III
- Re: [AMBER] Problem with the amber-14 compilation on Debian Jason Swails
- Re: [AMBER] number of frames in MMPBGBSA Soumendranath Bhakat
- Re: [AMBER] number of frames in MMPBGBSA Nitin Sharma
- [AMBER] dihedrals in CYT residue Sidney Elmer
- Re: [AMBER] handling long trajs for PCA and components plot Daniel Roe
- Re: [AMBER] dihedrals in CYT residue Sidney Elmer
- Re: [AMBER] dihedrals in CYT residue Jason Swails
- Re: [AMBER] dihedrals in CYT residue Sidney Elmer
- Re: [AMBER] number of frames in MMPBGBSA Soumendranath Bhakat
- [AMBER] Fwd: Re: Amber webminar Adrian Roitberg
- [AMBER] Processing a subset of mdcrd frames Eugene Yedvabny
- Re: [AMBER] Processing a subset of mdcrd frames Daniel Roe
- Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED Marek Maly
- Re: [AMBER] Processing a subset of mdcrd frames Eugene Yedvabny
- [AMBER] MMPBSA & mmpbsa_py_nabnmode frequent crashes Amir Shahmoradi
- Re: [AMBER] MMPBSA & mmpbsa_py_nabnmode frequent crashes Jason Swails
- Re: [AMBER] handling long trajs for PCA and components plot newamber list
- Re: [AMBER] Prepareing branched residue kurisaki
- Re: [AMBER] handling long trajs for PCA and components plot Daniel Roe
- Re: [AMBER] Processing a subset of mdcrd frames Daniel Roe
- [AMBER] how to generate a complete amino acid in suitable for the vacuum simulation 张明焜
- Re: [AMBER] handling long trajs for PCA and components plot newamber list
- [AMBER] PDB for 1-octanol molecules Mari Mak
Wednesday, 7 May 2014
- [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04 M. Reza Ganjalikhany
- [AMBER] Simulations using pmemd.cuda James Starlight
- [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" ahmed.sajid.stfc.ac.uk
- Re: [AMBER] Simulations using pmemd.cuda Marc van der Kamp
- Re: [AMBER] Simulations using pmemd.cuda James Starlight
- Re: [AMBER] Simulations using pmemd.cuda James Starlight
- Re: [AMBER] Simulations using pmemd.cuda Jason Swails
- Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" Jason Swails
- Re: [AMBER] PDB for 1-octanol molecules Jason Swails
- [AMBER] re-imaging bilayer Vijay Manickam Achari
- Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04 Jason Swails
- Re: [AMBER] how to generate a complete amino acid in suitable for the vacuum simulation David A Case
- Re: [AMBER] PDB for 1-octanol molecules David A Case
- [AMBER] FapydG parameters Norbert GARNIER
- Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04 David A Case
- Re: [AMBER] re-imaging bilayer Jason Swails
- Re: [AMBER] FapydG parameters Christina Bergonzo
- Re: [AMBER] FapydG parameters Carlos Simmerling
- Re: [AMBER] FapydG parameters Norbert GARNIER
- [AMBER] error in equilibration Lara rajam
- Re: [AMBER] error in equilibration Jason Swails
- Re: [AMBER] re-imaging bilayer Daniel Roe
- Re: [AMBER] handling long trajs for PCA and components plot Daniel Roe
- Re: [AMBER] how to generate a complete amino acid in suitable for the vacuum simulation FyD
- Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED FyD
- Re: [AMBER] PDB for 1-octanol molecules FyD
- [AMBER] Fwd: Re: PDB for 1-octanol molecules FyD
- Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" Ross Walker
- Re: [AMBER] Simulations using pmemd.cuda Ross Walker
- Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED Marek Maly
- Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" Scott Le Grand
- Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED FyD
- Re: [AMBER] Prepareing branched residue FyD
- Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED Marek Maly
- [AMBER] Question about structure factor? Xiaoquan Sun
- Re: [AMBER] Question about structure factor? David A Case
- Re: [AMBER] handling long trajs for PCA and components plot newamber list
- Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" ahmed.sajid.stfc.ac.uk
- [AMBER] please let me unsubscribe of this adm
- Re: [AMBER] Simulations using pmemd.cuda James Starlight
- [AMBER] Modeling systems with non-standard residues James Starlight
- Re: [AMBER] Membrane protein simulation James Starlight
Thursday, 8 May 2014
- Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" Ross Walker
- Re: [AMBER] Membrane protein simulation Ross Walker
- [AMBER] Error: invalid argument launching kernel kNLGenerateSpatialHash ASFARINA AMIR HASSAN
- Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" ahmed.sajid.stfc.ac.uk
- Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" ahmed.sajid.stfc.ac.uk
- Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" Ross Walker
- Re: [AMBER] Error: invalid argument launching kernel kNLGenerateSpatialHash Ross Walker
- [AMBER] syntax error and nab2c failed when using NAB Dongshan Wei
- [AMBER] Defining memory for QM/MM calculations Kshatresh Dutta Dubey
- [AMBER] sqm convergence failure Hannes Loeffler
- [AMBER] SolvateBox command George Patargias
- Re: [AMBER] Modeling systems with non-standard residues FyD
- Re: [AMBER] please let me unsubscribe of this Jason Swails
- Re: [AMBER] Modeling systems with non-standard residues Jason Swails
- Re: [AMBER] SolvateBox command Jason Swails
- Re: [AMBER] sqm convergence failure FyD
- Re: [AMBER] Defining memory for QM/MM calculations Jason Swails
- [AMBER] valve of VDW too high David Chen
- Re: [AMBER] valve of VDW too high Jason Swails
- Re: [AMBER] syntax error and nab2c failed when using NAB Jason Swails
- Re: [AMBER] Defining memory for QM/MM calculations Kshatresh Dutta Dubey
- Re: [AMBER] sqm convergence failure Hannes Loeffler
- [AMBER] creating quadruplex structure with NAB Ander
- Re: [AMBER] syntax error and nab2c failed when using NAB Dongshan Wei
- Re: [AMBER] sqm convergence failure Jason Swails
- Re: [AMBER] syntax error and nab2c failed when using NAB Jason Swails
- Re: [AMBER] syntax error and nab2c failed when using NAB Dongshan Wei
- Re: [AMBER] sqm convergence failure Hannes Loeffler
- Re: [AMBER] syntax error and nab2c failed when using NAB Jason Swails
- Re: [AMBER] syntax error and nab2c failed when using NAB David A Case
- Re: [AMBER] syntax error and nab2c failed when using NAB Dongshan Wei
- Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" Gustavo Seabra
- Re: [AMBER] sqm convergence failure Jason Swails
- Re: [AMBER] syntax error and nab2c failed when using NAB Dongshan Wei
- Re: [AMBER] syntax error and nab2c failed when using NAB Jason Swails
- [AMBER] mmpbsa: the nmode calculation Fengxue Li
- [AMBER] softcore potential flag Asaminew Haile
- Re: [AMBER] handling long trajs for PCA and components plot Daniel Roe
- Re: [AMBER] SolvateBox command George Patargias
- [AMBER] Alanine Scanning MMPBSA Aronica, Pietro
- [AMBER] Analysis of minimization stage Valentina Romano
- Re: [AMBER] Alanine Scanning MMPBSA Bill Miller III
- Re: [AMBER] Analysis of minimization stage Asaminew Haile
- Re: [AMBER] Analysis of minimization stage Daniel Roe
- Re: [AMBER] Analysis of minimization stage Valentina Romano
- Re: [AMBER] softcore potential flag David A Case
- Re: [AMBER] softcore potential flag Asaminew Haile
- Re: [AMBER] Alanine Scanning MMPBSA Aronica, Pietro
- Re: [AMBER] Alanine Scanning MMPBSA Bill Miller III
- Re: [AMBER] Alanine Scanning MMPBSA Aronica, Pietro
- Re: [AMBER] Analysis of minimization stage Daniel Roe
- Re: [AMBER] Alanine Scanning MMPBSA Jason Swails
- Re: [AMBER] softcore potential flag Brian Radak
- Re: [AMBER] sqm convergence failure hannes.loeffler.stfc.ac.uk
- [AMBER] Regarding Calculation of Hydrogen Bond Energy MOHD HOMAIDUR RAHMAN
- Re: [AMBER] Regarding Calculation of Hydrogen Bond Energy Jason Swails
- [AMBER] mmpbsa: the nmode calculation Fengxue Li
Friday, 9 May 2014
- Re: [AMBER] Analysis of minimization stage Valentina Romano
- Re: [AMBER] Alanine Scanning MMPBSA Aronica, Pietro
- Re: [AMBER] Alanine Scanning MMPBSA Jason Swails
- [AMBER] multinode NPT runs on GPU Sourav Purohit
- Re: [AMBER] Alanine Scanning MMPBSA Aronica, Pietro
- [AMBER] Siginificance of delta G Arunima Shilpi
- [AMBER] delta Ggas and Delta Gsolv Arunima Shilpi
- Re: [AMBER] multinode NPT runs on GPU Jason Swails
- Re: [AMBER] Siginificance of delta G Jason Swails
- Re: [AMBER] delta Ggas and Delta Gsolv Jason Swails
- Re: [AMBER] multinode NPT runs on GPU Sourav Purohit
- Re: [AMBER] multinode NPT runs on GPU Jason Swails
- Re: [AMBER] Analysis of minimization stage Daniel Roe
- Re: [AMBER] multinode NPT runs on GPU Sourav Purohit
- Re: [AMBER] multinode NPT runs on GPU Jason Swails
- Re: [AMBER] multinode NPT runs on GPU Brian Radak
- Re: [AMBER] Analysis of minimization stage Valentina Romano
- [AMBER] Analysis of evecs.dat file Ibrahim Said
- Re: [AMBER] Analysis of evecs.dat file newamber list
- [AMBER] pmemd.MPI failure George Tzotzos
- Re: [AMBER] pmemd.MPI failure James Maier
- [AMBER] Error when using PB implicit solvent in XMIN in NAB(PB Bomb in pb_init(): Allocation aborted) Guqin Shi
- Re: [AMBER] Error when using PB implicit solvent in XMIN in NAB(PB Bomb in pb_init(): Allocation aborted) Ray Luo, Ph.D.
- Re: [AMBER] Error when using PB implicit solvent in XMIN in NAB(PB Bomb in pb_init(): Allocation aborted) David A Case
- Re: [AMBER] sqm convergence failure David A Case
- Re: [AMBER] Error when using PB implicit solvent in XMIN in NAB(PB Bomb in pb_init(): Allocation aborted) Guqin Shi
- Re: [AMBER] Error when using PB implicit solvent in XMIN in NAB(PB Bomb in pb_init(): Allocation aborted) Guqin Shi
- Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04 M. Reza Ganjalikhany
Saturday, 10 May 2014
- Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04 David A Case
- [AMBER] AMBER : mmpbsa rms in nmode Fengxue Li
- Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04 M. Reza Ganjalikhany
- Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04 David A Case
- [AMBER] Additional random motion of com for unwrapped trajectory Sourav Purohit
Sunday, 11 May 2014
- [AMBER] Analysis of the mmpbsa output James Starlight
- Re: [AMBER] Modeling systems with non-standard residues James Starlight
- Re: [AMBER] Modeling systems with non-standard residues Brent Krueger
- Re: [AMBER] Additional random motion of com for unwrapped trajectory David A Case
- Re: [AMBER] handling long trajs for PCA and components plot newamber list
- [AMBER] Inputs QM/MM MD and MMGBSA Soumendranath Bhakat
- [AMBER] Amber workshops coming soon ? Saba Sulaiman
Monday, 12 May 2014
- Re: [AMBER] Modeling systems with non-standard residues James Starlight
- Re: [AMBER] Analysis of minimization stage Valentina Romano
- [AMBER] problem with nmode Fengxue Li
- [AMBER] Force field of antechamber , parm94 ? parm99? Jinfeng Huang
- [AMBER] QM/MM tutorial James Starlight
- Re: [AMBER] sqm convergence failure Hannes Loeffler
- Re: [AMBER] sqm convergence failure Jason Swails
- Re: [AMBER] QM/MM tutorial Jason Swails
- Re: [AMBER] Force field of antechamber , parm94 ? parm99? Jason Swails
- Re: [AMBER] Modeling systems with non-standard residues Parker de Waal
- Re: [AMBER] Analysis of minimization stage Jason Swails
- Re: [AMBER] Modeling systems with non-standard residues Jason Swails
- Re: [AMBER] Analysis of minimization stage David A Case
- Re: [AMBER] problem with nmode David A Case
- Re: [AMBER] Analysis of the mmpbsa output Jason Swails
- Re: [AMBER] Force field of antechamber , parm94 ? parm99? David A Case
- Re: [AMBER] Analysis of minimization stage Valentina Romano
- Re: [AMBER] sqm convergence failure David A Case
- Re: [AMBER] Analysis of minimization stage Jason Swails
- Re: [AMBER] Analysis of minimization stage David A Case
- Re: [AMBER] Analysis of minimization stage Valentina Romano
- Re: [AMBER] Analysis of minimization stage Jason Swails
- Re: [AMBER] Force field of antechamber , parm94 ? parm99? Jinfeng Huang
- Re: [AMBER] Force field of antechamber , parm94 ? parm99? Jason Swails
- Re: [AMBER] Analysis of minimization stage Valentina Romano
- Re: [AMBER] handling long trajs for PCA and components plot Daniel Roe
- Re: [AMBER] Analysis of minimization stage Daniel Roe
- [AMBER] about GPU memory requirements Thomas Evangelidis
- [AMBER] Recompile amber12 whit cuda 6.0 Hector A. Baldoni
- Re: [AMBER] about GPU memory requirements Jason Swails
- Re: [AMBER] Recompile amber12 whit cuda 6.0 Jason Swails
- Re: [AMBER] Recompile amber12 whit cuda 6.0 Ross Walker
- Re: [AMBER] about GPU memory requirements Ross Walker
- Re: [AMBER] Recompile amber12 whit cuda 6.0 Hector A. Baldoni
- [AMBER] get sqm Error when run antechamber Biao Ma
Tuesday, 13 May 2014
- [AMBER] Urgent: unable to generate files Faez Iqbal khan
- Re: [AMBER] Force field of antechamber , parm94 ? parm99? Jinfeng Huang
- Re: [AMBER] get sqm Error when run antechamber liu junjun
- Re: [AMBER] Urgent: unable to generate files liu junjun
- Re: [AMBER] Alanine Scanning MMPBSA Aronica, Pietro
- Re: [AMBER] Alanine Scanning MMPBSA Jason Swails
- Re: [AMBER] Urgent: unable to generate files Jason Swails
- Re: [AMBER] QM/MM tutorial James Starlight
- Re: [AMBER] Force field of antechamber , parm94 ? parm99? Jason Swails
- Re: [AMBER] QM/MM tutorial Marc van der Kamp
- Re: [AMBER] Modeling systems with non-standard residues James Starlight
- Re: [AMBER] Alanine Scanning MMPBSA Aronica, Pietro
- Re: [AMBER] QM/MM tutorial James Starlight
- [AMBER] REMD velocity information Saikat Dutta Chowdhury
- Re: [AMBER] QM/MM tutorial Marc van der Kamp
- [AMBER] exctracting indivdual frames into seperate files Nitin Sharma
- Re: [AMBER] exctracting indivdual frames into seperate files Jason Swails
- Re: [AMBER] REMD velocity information Jason Swails
- Re: [AMBER] QM/MM tutorial James Starlight
- Re: [AMBER] exctracting indivdual frames into seperate files Nitin Sharma
- Re: [AMBER] exctracting indivdual frames into seperate files Jason Swails
- Re: [AMBER] exctracting indivdual frames into seperate files Nitin Sharma
- Re: [AMBER] Analysis of minimization stage Valentina Romano
- Re: [AMBER] QM/MM tutorial Marc van der Kamp
- Re: [AMBER] Analysis of minimization stage Valentina Romano
- [AMBER] Installation AmberTools13 fabien.ibanez.modis.fr.netgrs.com
- [AMBER] Scaling of atomic mass of water molecules Manikanthan Bhavaraju
- Re: [AMBER] Scaling of atomic mass of water molecules Brian Radak
- Re: [AMBER] Scaling of atomic mass of water molecules Manikanthan Bhavaraju
- Re: [AMBER] Scaling of atomic mass of water molecules Brian Radak
- Re: [AMBER] Scaling of atomic mass of water molecules Manikanthan Bhavaraju
- Re: [AMBER] Scaling of atomic mass of water molecules Carlos Simmerling
- Re: [AMBER] Scaling of atomic mass of water molecules Manikanthan Bhavaraju
- Re: [AMBER] Analysis of minimization stage Daniel Roe
- Re: [AMBER] Scaling of atomic mass of water molecules Adrian Roitberg
- Re: [AMBER] Scaling of atomic mass of water molecules Manikanthan Bhavaraju
- Re: [AMBER] Scaling of atomic mass of water molecules Sergio R Aragon
- Re: [AMBER] get sqm Error when run antechamber Daniel Roe
- Re: [AMBER] Scaling of atomic mass of water molecules Manikanthan Bhavaraju
- [AMBER] Need help as a beginner MURAT OZTURK
- Re: [AMBER] Need help as a beginner Ilyas Yildirim
- Re: [AMBER] Need help as a beginner MURAT OZTURK
- Re: [AMBER] Need help as a beginner David A Case
- Re: [AMBER] Need help as a beginner MURAT OZTURK
- Re: [AMBER] Need help as a beginner Ilyas Yildirim
- Re: [AMBER] about GPU memory requirements Thomas Evangelidis
- Re: [AMBER] about GPU memory requirements Ross Walker
- Re: [AMBER] Need help as a beginner Jason Swails
- Re: [AMBER] Need help as a beginner MURAT OZTURK
- [AMBER] Installation Problem of AmberTools14 ujihara.ryuuta.47u.st.kyoto-u.ac.jp
Wednesday, 14 May 2014
- Re: [AMBER] QM/MM tutorial James Starlight
- [AMBER] AmberTools 14 compilation on OSX fails Fabian Glaser
- Re: [AMBER] QM/MM tutorial Mark Williamson
- Re: [AMBER] about GPU memory requirements Thomas Evangelidis
- Re: [AMBER] Analysis of the mmpbsa output James Starlight
- Re: [AMBER] QM/MM tutorial James Starlight
- [AMBER] thermodynamic integration (TI) simulation: pmemd of amber14 vs sander of amber11- vdw transformation Ying-Chieh Sun
- Re: [AMBER] QM/MM tutorial James Starlight
- Re: [AMBER] QM/MM tutorial Jason Swails
- Re: [AMBER] thermodynamic integration (TI) simulation: pmemd of amber14 vs sander of amber11- vdw transformation Jason Swails
- Re: [AMBER] Analysis of the mmpbsa output Jason Swails
- Re: [AMBER] Installation Problem of AmberTools14 Jason Swails
- Re: [AMBER] AmberTools 14 compilation on OSX fails Jason Swails
- Re: [AMBER] QM/MM tutorial Marc van der Kamp
- Re: [AMBER] QM/MM tutorial Jason Swails
- Re: [AMBER] Need help as a beginner Jason Swails
- Re: [AMBER] Need help as a beginner MURAT OZTURK
- Re: [AMBER] Need help as a beginner MURAT OZTURK
- Re: [AMBER] Need help as a beginner Jason Swails
- Re: [AMBER] Installation Problem of AmberTools14 ujihara.ryuuta.47u.st.kyoto-u.ac.jp
- Re: [AMBER] AmberTools 14 compilation on OSX fails Fabian Glaser
- Re: [AMBER] Analysis of minimization stage Valentina Romano
- Re: [AMBER] get sqm Error when run antechamber Biao Ma
- Re: [AMBER] AmberTools 14 compilation on OSX fails Jason Swails
- Re: [AMBER] Installation Problem of AmberTools14 Jason Swails
- Re: [AMBER] get sqm Error when run antechamber Jason Swails
- [AMBER] Protocol for multiple CPU+ single GPU run on a single node, MURAT OZTURK
- Re: [AMBER] Analysis of minimization stage David A Case
- Re: [AMBER] thermodynamic integration (TI) simulation: pmemd of amber14 vs sander of amber11- vdw transformation Ross Walker
- Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Jason Swails
- Re: [AMBER] QM/MM tutorial James Starlight
- Re: [AMBER] QM/MM tutorial James Starlight
- Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Ross Walker
- Re: [AMBER] QM/MM tutorial Daniel Roe
- Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, MURAT OZTURK
- Re: [AMBER] about GPU memory requirements Daniel Roe
- Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Jason Swails
- Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Ross Walker
- Re: [AMBER] about GPU memory requirements Ross Walker
- Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Scott Le Grand
- Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, MURAT OZTURK
- Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Ross Walker
- Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, MURAT OZTURK
- Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, James Maier
- Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Jason Swails
- Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Ross Walker
- Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, MURAT OZTURK
- Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Ross Walker
- Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, David A Case
- Re: [AMBER] get sqm Error when run antechamber Biao Ma
- [AMBER] TI(amber14's pmemd.cuda) on GPUs RE: thermodynamic integration (TI) simulation: pmemd of amber14 vs sander of amber11- vdw transformation Ying-Chieh Sun
- Re: [AMBER] TI(amber14's pmemd.cuda) on GPUs RE: thermodynamic integration (TI) simulation: pmemd of amber14 vs sander of amber11- vdw transformation Ross Walker
- Re: [AMBER] AmberTools 14 compilation on OSX fails Fabian Glaser
Thursday, 15 May 2014
- Re: [AMBER] Installation AmberTools13 fabien.ibanez.modis.fr.netgrs.com
- Re: [AMBER] QM/MM tutorial James Starlight
- Re: [AMBER] QM/MM tutorial Jason Swails
- Re: [AMBER] Installation AmberTools13 Jason Swails
- Re: [AMBER] QM/MM tutorial James Starlight
- Re: [AMBER] AmberTools 14 compilation on OSX fails Jason Swails
- [AMBER] Error: Could not compile with NetCDF Fortran interface gfortran-4.7 and amber14 Ben.Cossins.ucb.com
- Re: [AMBER] get sqm Error when run antechamber David A Case
- Re: [AMBER] AmberTools 14 compilation on OSX fails Fabian Glaser
- Re: [AMBER] AmberTools 14 compilation on OSX fails Fabian Glaser
- Re: [AMBER] Analysis of minimization stage Valentina Romano
- Re: [AMBER] AmberTools 14 compilation on OSX fails Jason Swails
- Re: [AMBER] AmberTools 14 compilation on OSX fails Fabian Glaser
- [AMBER] ALA and NALA charges in Amber03 and Amber99 Rossen Apostolov
- [AMBER] sander and processor sammia khatak
- [AMBER] when nastruct does NOT print the basepair information newamber list
- Re: [AMBER] Error: Could not compile with NetCDF Fortran interface gfortran-4.7 and amber14 Daniel Roe
- Re: [AMBER] when nastruct does NOT print the basepair information Daniel Roe
- Re: [AMBER] sander and processor Daniel Roe
- Re: [AMBER] ALA and NALA charges in Amber03 and Amber99 Jason Swails
- Re: [AMBER] Analysis of minimization stage Daniel Roe
- Re: [AMBER] sander and processor Jason Swails
- Re: [AMBER] ALA and NALA charges in Amber03 and Amber99 Rossen Apostolov
- Re: [AMBER] Analysis of minimization stage Jason Swails
- Re: [AMBER] ALA and NALA charges in Amber03 and Amber99 Jason Swails
- [AMBER] pairwise option in cpptraj newamber list
- [AMBER] torsion restraints not defined properly? Duggan, Brendan
- Re: [AMBER] torsion restraints not defined properly? Daniel Roe
- Re: [AMBER] pairwise option in cpptraj Daniel Roe
- [AMBER] AMBER Workshop Jun 2nd to 6th - Barcelona - Small number of additional places available. Ross Walker
- Re: [AMBER] torsion restraints not defined properly? David A Case
- Re: [AMBER] pairwise option in cpptraj newamber list
- Re: [AMBER] AMBER Digest, Vol 855, Issue 1 Duggan, Brendan
- Re: [AMBER] torsion restraints not defined properly? Daniel Roe
- Re: [AMBER] pairwise option in cpptraj Daniel Roe
- Re: [AMBER] SolvateBox command Bill Ross
Friday, 16 May 2014
- Re: [AMBER] QM/MM tutorial James Starlight
- Re: [AMBER] get sqm Error when run antechamber Biao Ma
- [AMBER] acetylated lysine - OXT berin karaman
- Re: [AMBER] QM/MM tutorial James Starlight
- Re: [AMBER] QM/MM tutorial Marc van der Kamp
- Re: [AMBER] QM/MM tutorial James Starlight
- Re: [AMBER] QM/MM tutorial James Starlight
- Re: [AMBER] QM/MM tutorial Marc van der Kamp
- Re: [AMBER] Analysis of minimization stage Valentina Romano
- Re: [AMBER] acetylated lysine - OXT David A Case
- Re: [AMBER] Analysis of minimization stage David A Case
- Re: [AMBER] acetylated lysine - OXT berin karaman
- Re: [AMBER] Analysis of minimization stage Valentina Romano
- Re: [AMBER] Analysis of minimization stage Jason Swails
- Re: [AMBER] acetylated lysine - OXT Jason Swails
- Re: [AMBER] Analysis of minimization stage Valentina Romano
- [AMBER] parmchk2 segfaults Hannes Loeffler
- Re: [AMBER] acetylated lysine - OXT berin karaman
- Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions Ben Ahmady
- Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions Brian Radak
- Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions Ben Ahmady
- Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions Brian Radak
- [AMBER] Problem with Decomposition of Binding Free Energy loue chen
- Re: [AMBER] Saturday Bill Ross
- Re: [AMBER] Analysis of minimization stage David A Case
- Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions Jason Swails
- Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions Jason Swails
- Re: [AMBER] Problem with Decomposition of Binding Free Energy Jason Swails
- [AMBER] How to plot Eigenvectors against % Positional Fluctuations Yip Yew Mun
- [AMBER] Problem in generating xml param files Sushi Shilpa
- [AMBER] error in minimization Sajda Ashraf
Saturday, 17 May 2014
- [AMBER] MMPBSA Soumya Lipsa Rath
- Re: [AMBER] MMPBSA Bill Miller III
- [AMBER] Extending MMPBSA Arun Kumar Somavarapu
- Re: [AMBER] Extending MMPBSA Bill Miller III
- Re: [AMBER] MMPBSA Soumendranath Bhakat
- [AMBER] Script for Calculating RMSIP Yip Yew Mun
- [AMBER] Bad prmtop during density run Kshatresh Dutta Dubey
- [AMBER] Unit cell vectors are NOT rotated; imaging will not be possible newamber list
- Re: [AMBER] Bad prmtop during density run Jason Swails
- Re: [AMBER] Unit cell vectors are NOT rotated; imaging will not be possible Jason Swails
- Re: [AMBER] Unit cell vectors are NOT rotated; imaging will not be possible newamber list
- Re: [AMBER] error in minimization David A Case
- Re: [AMBER] Script for Calculating RMSIP Hector A. Baldoni
Sunday, 18 May 2014
- Re: [AMBER] QM/MM tutorial James Starlight
- [AMBER] QM/MM based binding free energy analysis AMBER Soumendranath Bhakat
- Re: [AMBER] QM/MM based binding free energy analysis AMBER Nitin Sharma
- Re: [AMBER] QM/MM based binding free energy analysis AMBER Soumendranath Bhakat
- Re: [AMBER] QM/MM based binding free energy analysis AMBER Nitin Sharma
- Re: [AMBER] QM/MM based binding free energy analysis AMBER Soumendranath Bhakat
- Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions Ben Ahmady
- [AMBER] Abdullahi Abubakar invited you to check out Dropbox Dropbox
- [AMBER] Fwd: MMPBSA Soumya Lipsa Rath
- Re: [AMBER] error in minimization Sajda Ashraf
- [AMBER] sander restart sammia khatak
Monday, 19 May 2014
- [AMBER] antechamber with Au atom giulia palermo
- Re: [AMBER] sander restart Soumendranath Bhakat
- [AMBER] can “NAB: Molecular mechanics and dynamics” do qmmm caculation? 张明焜
- Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions Ben Ahmady
- Re: [AMBER] sander restart sammia khatak
- Re: [AMBER] sander restart Soumendranath Bhakat
- Re: [AMBER] QM/MM based binding free energy analysis AMBER Nitin Sharma
- Re: [AMBER] sander restart sammia khatak
- Re: [AMBER] sander restart Soumendranath Bhakat
- Re: [AMBER] QM/MM based binding free energy analysis AMBER Soumendranath Bhakat
- Re: [AMBER] error in minimization David A Case
- Re: [AMBER] antechamber with Au atom David A Case
- Re: [AMBER] can “NAB: Molecular mechanics and dynamics” do qmmm caculation? David A Case
- [AMBER] About the reproducibility of pmemd Val Yu
- Re: [AMBER] QM/MM tutorial Marc van der Kamp
- [AMBER] NH4+ Thomas Exner
- Re: [AMBER] About the reproducibility of pmemd Jason Swails
- Re: [AMBER] About the reproducibility of pmemd David A Case
- Re: [AMBER] NH4+ Alessandro Contini
- Re: [AMBER] Fwd: MMPBSA Jason Swails
- Re: [AMBER] NH4+ Thomas Exner
- Re: [AMBER] NH4+ Alessandro Contini
- Re: [AMBER] Script for Calculating RMSIP Daniel Roe
- Re: [AMBER] How to plot Eigenvectors against % Positional Fluctuations Daniel Roe
- [AMBER] Antechamber CHRISTOPHER PATRICK MCNARY
- Re: [AMBER] handling long trajs for PCA and components plot Daniel Roe
- Re: [AMBER] antechamber with Au atom FyD
- Re: [AMBER] NH4+ FyD
- [AMBER] Problem in parallel version of pmemd.cuda Sanjib Paul
- Re: [AMBER] Problem in parallel version of pmemd.cuda Ross Walker
- Re: [AMBER] About the reproducibility of pmemd Ross Walker
- [AMBER] conversion force constant giulia palermo
- Re: [AMBER] conversion force constant James Maier
- Re: [AMBER] Problem in parallel version of pmemd.cuda David A Case
- [AMBER] Announcement: New GLYCAM-Web Lachele Foley
- Re: [AMBER] Fwd: MMPBSA Soumya Lipsa Rath
Tuesday, 20 May 2014
- [AMBER] Constant protein diffusion across PB boundaties James Starlight
- Re: [AMBER] SQM: How to extract the charge density of sqm runs? Marc van der Kamp
- Re: [AMBER] Fwd: MMPBSA Jason Swails
- Re: [AMBER] Constant protein diffusion across PB boundaties Jason Swails
- Re: [AMBER] Additional random motion of com for unwrapped trajectory Sourav Purohit
- Re: [AMBER] Constant protein diffusion across PB boundaties Jason Swails
- Re: [AMBER] Fwd: MMPBSA Soumya Lipsa Rath
- Re: [AMBER] Fwd: MMPBSA Jason Swails
- [AMBER] 答复: About the reproducibility of pmemd Val Yu
- Re: [AMBER] Alanine Scanning MMPBSA Aronica, Pietro
- Re: [AMBER] Problem in parallel version of pmemd.cuda Sanjib Paul
- Re: [AMBER] 答复: About the reproducibility of pmemd Jason Swails
- Re: [AMBER] Alanine Scanning MMPBSA Jason Swails
- Re: [AMBER] Fwd: MMPBSA Soumya Lipsa Rath
- Re: [AMBER] Problem in parallel version of pmemd.cuda Jason Swails
- Re: [AMBER] Analysis of minimization stage Valentina Romano
- Re: [AMBER] Analysis of minimization stage Brian Radak
- Re: [AMBER] Problem in parallel version of pmemd.cuda Daniel Roe
- Re: [AMBER] sqm convergence failure Gerald Monard
- [AMBER] Trajectory analysis using pptraj James Starlight
- Re: [AMBER] Problem in parallel version of pmemd.cuda Sanjib Paul
- Re: [AMBER] sqm convergence failure David A Case
- Re: [AMBER] Problem in parallel version of pmemd.cuda Jason Swails
- Re: [AMBER] Trajectory analysis using pptraj Daniel Roe
- Re: [AMBER] sqm convergence failure Jason Swails
- [AMBER] Error in setting irest=1 Valentina Romano
- Re: [AMBER] Problem in parallel version of pmemd.cuda Sanjib Paul
- [AMBER] csurften requirement for semiisotropic coupling Eric Hill
- Re: [AMBER] Error in setting irest=1 Daniel Roe
- [AMBER] cant run ntp=3 without csurften Eric Hill
- Re: [AMBER] Problem in parallel version of pmemd.cuda Jason Swails
- Re: [AMBER] cant run ntp=3 without csurften Jason Swails
- Re: [AMBER] cant run ntp=3 without csurften Benjamin D Madej
- Re: [AMBER] cant run ntp=3 without csurften Benjamin D Madej
- Re: [AMBER] cant run ntp=3 without csurften Eric Hill
- Re: [AMBER] torsion restraints not defined properly? Duggan, Brendan
- Re: [AMBER] cant run ntp=3 without csurften Ross Walker
- Re: [AMBER] cant run ntp=3 without csurften Eric Hill
- [AMBER] secondary structure calculation using Cpptraj Marlet Martinez
- Re: [AMBER] cant run ntp=3 without csurften Ross Walker
- Re: [AMBER] sqm convergence failure FyD
- Re: [AMBER] secondary structure calculation using Cpptraj Daniel Roe
- [AMBER] Attempting to modify Amber Nelson Max
- Re: [AMBER] Script for Calculating RMSIP Yip Yew Mun
- [AMBER] error in mdcrd file Sajda Ashraf
Wednesday, 21 May 2014
- Re: [AMBER] Error in setting irest=1 Soumendranath Bhakat
- Re: [AMBER] secondary structure calculation using Cpptraj Marlet Martinez
- Re: [AMBER] NH4+ Thomas Exner
- Re: [AMBER] NH4+ Alessandro Contini
- Re: [AMBER] conversion force constant giulia palermo
- Re: [AMBER] conversion force constant Jason Swails
- [AMBER] Simulation of the protein with internal water James Starlight
- [AMBER] Low energy path Hector A. Baldoni
- [AMBER] Peptides moving out of the water box Ilias Patmanidis
- [AMBER] Temperature rises to 4000K during NVT equilibration Indrajit Deb
- Re: [AMBER] Peptides moving out of the water box Daniel Roe
- Re: [AMBER] Temperature rises to 4000K during NVT equilibration Daniel Roe
- Re: [AMBER] Low energy path James Maier
- Re: [AMBER] Temperature rises to 4000K during NVT equilibration Indrajit Deb
- Re: [AMBER] Temperature rises to 4000K during NVT equilibration Daniel Roe
- Re: [AMBER] ALA and NALA charges in Amber03 and Amber99 Rossen Apostolov
- Re: [AMBER] Temperature rises to 4000K during NVT equilibration David A Case
- Re: [AMBER] ALA and NALA charges in Amber03 and Amber99 Jason Swails
- Re: [AMBER] Temperature rises to 4000K during NVT equilibration Indrajit Deb
- Re: [AMBER] Trajectory analysis using pptraj James Starlight
- Re: [AMBER] Trajectory analysis using pptraj Vlad Cojocaru
- Re: [AMBER] Trajectory analysis using pptraj Jason Swails
- Re: [AMBER] Temperature rises to 4000K during NVT equilibration Jason Swails
- Re: [AMBER] Temperature rises to 4000K during NVT equilibration Indrajit Deb
- Re: [AMBER] Temperature rises to 4000K during NVT equilibration Daniel Roe
- [AMBER] Interactions across the periodic box boundaries Eugene Yedvabny
- Re: [AMBER] Interactions across the periodic box boundaries Daniel Roe
- Re: [AMBER] handling long trajs for PCA and components plot newamber list
- Re: [AMBER] Interactions across the periodic box boundaries Jason Swails
- Re: [AMBER] Low energy path Hector A. Baldoni
- [AMBER] About the chamber in Ambertools 14 Yeng-Tseng Wang
- Re: [AMBER] About the chamber in Ambertools 14 Ross Walker
Thursday, 22 May 2014
- Re: [AMBER] About the chamber in Ambertools 14 Yeng-Tseng Wang
- Re: [AMBER] QM/MM tutorial James Starlight
- [AMBER] antechamber error Sajda Ashraf
- Re: [AMBER] QM/MM tutorial Jason Swails
- Re: [AMBER] antechamber error Jason Swails
- Re: [AMBER] QM/MM tutorial James Starlight
- Re: [AMBER] QM/MM tutorial Jason Swails
- Re: [AMBER] QM/MM tutorial James Starlight
- Re: [AMBER] QM/MM tutorial Soumendranath Bhakat
- Re: [AMBER] Trajectory analysis using pptraj James Starlight
- Re: [AMBER] Trajectory analysis using pptraj Jason Swails
- Re: [AMBER] QM/MM tutorial Jason Swails
- [AMBER] z-axis restraints Pierpaolo Cacciotto
- Re: [AMBER] QM/MM tutorial Ross Walker
- Re: [AMBER] QM/MM tutorial Soumendranath Bhakat
- Re: [AMBER] Attempting to modify Amber David A Case
- [AMBER] mmpbsa zahra khatti
- Re: [AMBER] mmpbsa Jason Swails
- [AMBER] mmpbsa Lara rajam
- [AMBER] prmtop error Lara rajam
- Re: [AMBER] prmtop error Soumendranath Bhakat
- [AMBER] in vacuo dynamics Massimiliano Porrini
- Re: [AMBER] in vacuo dynamics Jason Swails
- Re: [AMBER] prmtop error Jason Swails
- Re: [AMBER] prmtop error Thomas Cheatham
- Re: [AMBER] prmtop error Jason Swails
- Re: [AMBER] About the chamber in Ambertools 14 Yeng-Tseng Wang
- [AMBER] Problem in loading leaprc.zinc amin.imtech.res.in
Friday, 23 May 2014
- Re: [AMBER] in vacuo dynamics Massimiliano Porrini
- Re: [AMBER] in vacuo dynamics Massimiliano Porrini
- [AMBER] Secondary Structure Script Soumendranath Bhakat
- [AMBER] SASA calculation Soumendranath Bhakat
- Re: [AMBER] in vacuo dynamics Jason Swails
- Re: [AMBER] SASA calculation Jason Swails
- Re: [AMBER] Problem in loading leaprc.zinc Jason Swails
- Re: [AMBER] SASA calculation Soumendranath Bhakat
- Re: [AMBER] SASA calculation Soumendranath Bhakat
- Re: [AMBER] SASA calculation Asaminew Haile
- [AMBER] SASA error Soumendranath Bhakat
- Re: [AMBER] Problem in loading leaprc.zinc amin.imtech.res.in
- Re: [AMBER] in vacuo dynamics Massimiliano Porrini
- Re: [AMBER] in vacuo dynamics Jason Swails
- Re: [AMBER] SASA error Asaminew Haile
- Re: [AMBER] SASA error Soumendranath Bhakat
- [AMBER] compiling iAPBS and sander.APBS? Brian Radak
Saturday, 24 May 2014
- [AMBER] I want to know about formula of RESP Charge in the Amber Kim TaeHwan
- Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 Jan-Philip Gehrcke
- Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 Ray Luo, Ph.D.
- [AMBER] Topology and Corresponding PDB Amber Soumendranath Bhakat
- Re: [AMBER] Topology and Corresponding PDB Amber Jason Swails
- Re: [AMBER] compiling iAPBS and sander.APBS? Robert Konecny
Sunday, 25 May 2014
- Re: [AMBER] Trajectory analysis using pptraj James Starlight
- [AMBER] Accelerated MD in Amber James Starlight
- Re: [AMBER] in vacuo dynamics Massimiliano Porrini
- [AMBER] MD at constant pH and high temperature Sangita Kachhap
- Re: [AMBER] compiling iAPBS and sander.APBS? Brian Radak
- Re: [AMBER] in vacuo dynamics Robert McGibbon
- [AMBER] How to define the direction of the force in SMD method? Cuiyl
- Re: [AMBER] compiling iAPBS and sander.APBS? Robert Konecny
- [AMBER] MD at pH5 and 50-55 degree celcius Sangita Kachhap
Monday, 26 May 2014
- [AMBER] Loop refirement James Starlight
- Re: [AMBER] in vacuo dynamics Massimiliano Porrini
- Re: [AMBER] MD at constant pH and high temperature David A Case
- Re: [AMBER] MD at constant pH and high temperature Sangita Kachhap
- Re: [AMBER] MD at constant pH and high temperature. . Bharatham, Nagakumar
- Re: [AMBER] MD at constant pH and high temperature. . Sangita Kachhap
- Re: [AMBER] MD at constant pH and high temperature Adrian Roitberg
- Re: [AMBER] MD at constant pH and high temperature Sangita Kachhap
- [AMBER] PCA and the corresponding pdb Ibrahim Said
- Re: [AMBER] MD at constant pH and high temperature Jason Swails
- Re: [AMBER] in vacuo dynamics Jason Swails
- Re: [AMBER] in vacuo dynamics Jason Swails
- Re: [AMBER] How to define the direction of the force in SMD method? Jason Swails
- Re: [AMBER] in vacuo dynamics Robert McGibbon
- [AMBER] OpenMM Performance (was Re: in vacuo dynamics) Jason Swails
- [AMBER] MMPBSA: Per Residue vs Pairwise decomposition Calculation Rodriguez, Yoel
- [AMBER] Residue Pairing ih MMPBSA calculation Arunima Shilpi
- Re: [AMBER] How to define the direction of the force in SMD method? Cuiyl
Tuesday, 27 May 2014
- [AMBER] 3NKB5 王珍
- Re: [AMBER] 3NKB5 Jason Swails
- Re: [AMBER] Residue Pairing ih MMPBSA calculation Jason Swails
- Re: [AMBER] Residue Pairing ih MMPBSA calculation Soumendranath Bhakat
- Re: [AMBER] Residue Pairing ih MMPBSA calculation Soumendranath Bhakat
- Re: [AMBER] compiling iAPBS and sander.APBS? Brian Radak
- Re: [AMBER] in vacuo dynamics Massimiliano Porrini
- Re: [AMBER] in vacuo dynamics Jason Swails
- Re: [AMBER] Trajectory analysis using pptraj Daniel Roe
- Re: [AMBER] Accelerated MD in Amber Daniel Roe
- Re: [AMBER] in vacuo dynamics Massimiliano Porrini
- Re: [AMBER] MD at pH5 and 50-55 degree celcius Daniel Roe
- Re: [AMBER] PCA and the corresponding pdb Daniel Roe
- [AMBER] rmsd of multiple trajectories with different topologies and sizes but same reference Brian Radak
- Re: [AMBER] rmsd of multiple trajectories with different topologies and sizes but same reference Daniel Roe
- Re: [AMBER] rmsd of multiple trajectories with different topologies and sizes but same reference Brian Radak
- Re: [AMBER] MD at pH5 and 50-55 degree celcius Sangita Kachhap
- [AMBER] Disulfide Bond Info and XMIN Stuck Problems Guqin Shi
- Re: [AMBER] MD at constant pH and high temperature Sangita Kachhap
- [AMBER] MMPBSA: Per Residue vs Pairwise decomposition Calculation(idecomp= 2 o idecomp=4) Rodriguez, Yoel
- [AMBER] MMPBSA Hallel Freedman
- Re: [AMBER] OpenMM Performance (was Re: in vacuo dynamics) Scott Le Grand
- Re: [AMBER] MMPBSA Ray Luo, Ph.D.
- Re: [AMBER] PCA and the corresponding pdb Ibrahim Said
- Re: [AMBER] PCA and the corresponding pdb Daniel Roe
- Re: [AMBER] OpenMM Performance (was Re: in vacuo dynamics) Robert McGibbon
- Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems David A Case
- Re: [AMBER] OpenMM Performance (was Re: in vacuo dynamics) Jason Swails
- Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems Guqin Shi
- Re: [AMBER] OpenMM Performance (was Re: in vacuo dynamics) Scott Le Grand
- [AMBER] print residue Arunima Shilpi
- [AMBER] zinc partial charges Nash, Anthony
Wednesday, 28 May 2014
- Re: [AMBER] Accelerated MD in Amber James Starlight
- Re: [AMBER] Loop refirement James Starlight
- Re: [AMBER] Loop refirement Vlad Cojocaru
- Re: [AMBER] PCA and the corresponding pdb Soumendranath Bhakat
- Re: [AMBER] print residue Jason Swails
- Re: [AMBER] print residue Soumendranath Bhakat
- Re: [AMBER] 3NKB5 王珍
- [AMBER] command to check non bonded interactions like vander waal's interactions Nitin Sharma
- Re: [AMBER] command to check non bonded interactions like vander waal's interactions Jason Swails
- Re: [AMBER] Alanine Scanning MMPBSA Aronica, Pietro
- Re: [AMBER] PCA and the corresponding pdb Daniel Roe
- Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems David A Case
- Re: [AMBER] command to check non bonded interactions like vander waal's interactions Soumendranath Bhakat
- Re: [AMBER] Alanine Scanning MMPBSA Jason Swails
- Re: [AMBER] Accelerated MD in Amber Daniel Roe
- Re: [AMBER] 3NKB5 王珍
- Re: [AMBER] 3NKB5 Jason Swails
- Re: [AMBER] 3NKB5 王珍
- Re: [AMBER] 3NKB5 Jason Swails
- [AMBER] amber in namd Lara rajam
- Re: [AMBER] amber in namd Jason Swails
- Re: [AMBER] how to protonate phosphate groups of nucleotides Valentina D'Atri
- Re: [AMBER] Accelerated MD in Amber James Starlight
- Re: [AMBER] MMPBSA Hallel Freedman
- [AMBER] Contributing new water models Lee-Ping Wang
- Re: [AMBER] Accelerated MD in Amber Christina Bergonzo
- Re: [AMBER] MMPBSA Hallel Freedman
- Re: [AMBER] Contributing new water models Jason Swails
- Re: [AMBER] Contributing new water models Lee-Ping Wang
- Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems Guqin Shi
- Re: [AMBER] MMPBSA Ray Luo, Ph.D.
- Re: [AMBER] MMPBSA Hallel Freedman
- Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems David A Case
- Re: [AMBER] 3NKB5 王珍
- Re: [AMBER] Contributing new water models David A Case
- Re: [AMBER] MMPBSA Hallel Freedman
- [AMBER] print residue Arunima Shilpi
- Re: [AMBER] print residue Soumendranath Bhakat
- Re: [AMBER] zinc partial charges FyD
Thursday, 29 May 2014
- Re: [AMBER] how to protonate phosphate groups of nucleotides FyD
- [AMBER] Query regarding Amber Advance Tutorial 17 Kshatresh Dutta Dubey
- Re: [AMBER] Query regarding Amber Advance Tutorial 17 Jason Swails
- [AMBER] MMPBSA_complex.mdcrd.0 error mahnam karim
- Re: [AMBER] Query regarding Amber Advance Tutorial 17 Kshatresh Dutta Dubey
- Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems Guqin Shi
- Re: [AMBER] MMPBSA Ray Luo, Ph.D.
- Re: [AMBER] MMPBSA_complex.mdcrd.0 error Ray Luo, Ph.D.
- Re: [AMBER] MMPBSA Hallel Freedman
- Re: [AMBER] MMPBSA Jason Swails
- Re: [AMBER] MMPBSA Hallel Freedman
- Re: [AMBER] MMPBSA Jason Swails
- Re: [AMBER] MMPBSA Hallel Freedman
- Re: [AMBER] MMPBSA Ray Luo, Ph.D.
- Re: [AMBER] MMPBSA Hallel Freedman
- [AMBER] protonate question 王珍
- Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Keiran Rowell
Friday, 30 May 2014
- [AMBER] sudden and rapid configuration change in NVT simulation yjlee
- Re: [AMBER] sudden and rapid configuration change in NVT simulation Soumendranath Bhakat
- [AMBER] Problem in restarting simulation from restart file Kshatresh Dutta Dubey
- Re: [AMBER] Problem in restarting simulation from restart file Jason Swails
- Re: [AMBER] protonate question Jason Swails
- Re: [AMBER] Alanine Scanning MMPBSA Jason Swails
- Re: [AMBER] Alanine Scanning MMPBSA Jason Swails
- [AMBER] periodic box buffer zone Paulsen, Janet
- Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Ross Walker
- [AMBER] amber in namd Lara rajam
- Re: [AMBER] periodic box buffer zone Brian Radak
- Re: [AMBER] amber in namd Jason Swails
- Re: [AMBER] amber in namd amin.imtech.res.in
- [AMBER] Parametrization of non-standart residues James Starlight
- Re: [AMBER] Parametrization of non-standart residues Jason Swails
- Re: [AMBER] Parametrization of non-standart residues James Starlight
- Re: [AMBER] Parametrization of non-standart residues James Starlight
- Re: [AMBER] Parametrization of non-standart residues Parker de Waal
- Re: [AMBER] Parametrization of non-standart residues James Starlight
- [AMBER] request for help in plotting distance matrix plot Robin Jain
- Re: [AMBER] request for help in plotting distance matrix plot Soumendranath Bhakat
Saturday, 31 May 2014
- Re: [AMBER] protonate question 王珍
- Re: [AMBER] Parametrization of non-standart residues FyD
- Re: [AMBER] Parametrization of non-standart residues James Starlight
- Re: [AMBER] Parametrization of non-standart residues Parker de Waal
- [AMBER] error in plot of interaction energy in xmgrace Arunima Shilpi
- Re: [AMBER] Parametrization of non-standart residues James Starlight
- Re: [AMBER] error in plot of interaction energy in xmgrace Soumendranath Bhakat
- Re: [AMBER] Parametrization of non-standart residues FyD
- Re: [AMBER] Parametrization of non-standart residues Jason Swails
- Re: [AMBER] request for help in plotting distance matrix plot Jason Swails
- [AMBER] problem using pmemd.cuda with barostat=2 option Asaminew Haile
- [AMBER] sander QM/MM with terachem using MPI Daniel Hollas
- Re: [AMBER] problem using pmemd.cuda with barostat=2 option Jason Swails
- Re: [AMBER] problem using pmemd.cuda with barostat=2 option Asaminew Haile
- [AMBER] ff99SB-ildn-nmr Nihal Korkmaz
- Re: [AMBER] ff99SB-ildn-nmr Jason Swails

Last message date: Sat May 31 2014 - 12:30:02 PDT
Archived on: Fri May 03 2024 - 05:54:46 PDT

Amber Archive May 2014 by date