Amber Archive Jun 2014: by date

Sunday, 1 June 2014
- [AMBER] calculation diffusion coefficient Sohag Biswas
- Re: [AMBER] calculation diffusion coefficient David A Case
- [AMBER] FF12SB (and FF14?) - any benchmarks/evidence of its quality? Marc van der Kamp
- [AMBER] error in plot of interaction energy in xmgrace Arunima Shilpi
- Re: [AMBER] error in plot of interaction energy in xmgrace Asaminew Haile
- Re: [AMBER] request for help in plotting distance matrix plot Daniel Roe
- Re: [AMBER] request for help in plotting distance matrix plot Soumendranath Bhakat
- Re: [AMBER] FF12SB (and FF14?) - any benchmarks/evidence of its quality? Hai Nguyen
- Re: [AMBER] FF12SB (and FF14?) - any benchmarks/evidence of its quality? Carlos Simmerling
- Re: [AMBER] error in plot of interaction energy in xmgrace Soumendranath Bhakat
- [AMBER] defining reaction coordinate for umbrella sampling Jorgen Simonsen
- Re: [AMBER] defining reaction coordinate for umbrella sampling Jason Swails
- [AMBER] Ligand movement in protein cavatiy Jurgens de Bruin
- Re: [AMBER] Ligand movement in protein cavatiy Aldo Segura
- Re: [AMBER] Ligand movement in protein cavatiy Jurgens de Bruin
- [AMBER] plot in xmgrace (interaction energy per residues) Arunima Shilpi
- Re: [AMBER] sudden and rapid configuration change in NVT simulation yjlee
Monday, 2 June 2014
- Re: [AMBER] Contributing new water models adm
- [AMBER] Pressure fluctuation problem during NPT simulation Saikat Dutta chowdhury
- Re: [AMBER] plot in xmgrace (interaction energy per residues) David A Case
- [AMBER] Using MM-PBSA to find binding free energy for Zif 268-DNA complex Roza M
- Re: [AMBER] Contributing new water models Jason Swails
- Re: [AMBER] sudden and rapid configuration change in NVT simulation Jason Swails
- Re: [AMBER] Ligand movement in protein cavatiy Jason Swails
- Re: [AMBER] Using MM-PBSA to find binding free energy for Zif 268-DNA complex Jason Swails
- Re: [AMBER] Ligand movement in protein cavatiy Jurgens de Bruin
- Re: [AMBER] Pressure fluctuation problem during NPT simulation Jason Swails
- Re: [AMBER] Pressure fluctuation problem during NPT simulation Saikat Dutta chowdhury
- Re: [AMBER] Ligand movement in protein cavatiy Jason Swails
- [AMBER] Regarding molecule's breaking during simulation. richa anand
- Re: [AMBER] Ligand movement in protein cavatiy Soumendranath Bhakat
- Re: [AMBER] Using MM-PBSA to find binding free energy for Zif 268-DNA complex Roza M
- Re: [AMBER] Regarding molecule's breaking during simulation. Jason Swails
- Re: [AMBER] Using MM-PBSA to find binding free energy for Zif 268-DNA complex Soumendranath Bhakat
- Re: [AMBER] Using MM-PBSA to find binding free energy for Zif 268-DNA complex Jason Swails
- Re: [AMBER] Ligand movement in protein cavatiy Jurgens de Bruin
- Re: [AMBER] Ligand movement in protein cavatiy Aldo Segura
- [AMBER] Using MM-PBSA to find binding free energy for Zif268-DNA complex Roza M
- [AMBER] image distances newamber list
- Re: [AMBER] image distances Daniel Roe
- [AMBER] mmpbsa.py zahra khatti
- Re: [AMBER] image distances newamber list
- [AMBER] error in MMPBSA Lara rajam
- [AMBER] WaterBox Dimensions Ahmed Ayoub
- [AMBER] Distance matrix time series Eugene Yedvabny
- Re: [AMBER] error in MMPBSA Ray Luo, Ph.D.
- [AMBER] Mistake in water density Vu Truong
- Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Keiran Rowell
- Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Scott Le Grand
- Re: [AMBER] SolvateBox command Bill Ross
- [AMBER] Error in cpptraj remlog command Eugene Yedvabny
- Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Keiran Rowell
- Re: [AMBER] Error in cpptraj remlog command Daniel Roe
- Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Scott Le Grand
- Re: [AMBER] Ligand movement in protein cavatiy Jurgens de Bruin
- [AMBER] help in grid command Robin Jain
- Re: [AMBER] sudden and rapid configuration change in NVT simulation yjlee
Tuesday, 3 June 2014
- [AMBER] help in calculating Angular distribution function Robin Jain
- [AMBER] active site water cluster analysis Ahmet yıldırım
- [AMBER] Could not find angle parameter: S - S - S Sangita Kachhap
- Re: [AMBER] Could not find angle parameter: S - S - S Hector A. Baldoni
- Re: [AMBER] Could not find angle parameter: S - S - S Sangita Kachhap
- [AMBER] sander14 MPI produces different results depending on number of used cores David Abia
- Re: [AMBER] WaterBox Dimensions David A Case
- Re: [AMBER] Mistake in water density David A Case
- Re: [AMBER] help in grid command Jason Swails
- Re: [AMBER] Parametrization of non-standart residues James Starlight
- Re: [AMBER] sander14 MPI produces different results depending on number of used cores David A Case
- Re: [AMBER] Parametrization of non-standart residues Parker de Waal
- Re: [AMBER] sudden and rapid configuration change in NVT simulation Jason Swails
- Re: [AMBER] sudden and rapid configuration change in NVT simulation Soumendranath Bhakat
- Re: [AMBER] sudden and rapid configuration change in NVT simulation Daniel Roe
- [AMBER] MMPBSA error zahra khatti
- Re: [AMBER] Distance matrix time series Daniel Roe
- [AMBER] QM/MM and spin parameter Jinfeng Huang
- Re: [AMBER] MMPBSA error Jason Swails
- Re: [AMBER] Parametrization of non-standart residues James Starlight
- Re: [AMBER] QM/MM and spin parameter Brian Radak
- Re: [AMBER] QM/MM and spin parameter Jason Swails
- [AMBER] (probably) benign error when writing iapbs-pot.dx files with sander.APBS Brian Radak
- [AMBER] Parametrization of the protein with the assigned protonation states James Starlight
- Re: [AMBER] Parametrization of the protein with the assigned protonation states Jason Swails
- Re: [AMBER] Error in cpptraj remlog command Daniel Roe
- [AMBER] MTKPP installation error Kshatresh Dutta Dubey
- Re: [AMBER] MTKPP installation error Jason Swails
- Re: [AMBER] MTKPP installation error Kshatresh Dutta Dubey
- Re: [AMBER] MMPBSA error zahra khatti
- [AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10 Thomas Evangelidis
- Re: [AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10 Jason Swails
- [AMBER] donor and acceptor group in hbond Arunima Shilpi
- Re: [AMBER] MTKPP installation error Kshatresh Dutta Dubey
- [AMBER] set up for the ScaledMD zhou gong
Wednesday, 4 June 2014
- [AMBER] Calculating absolute binding free energy menwer momo
- Re: [AMBER] set up for the ScaledMD Neha Gandhi
- [AMBER] GAFFlipid parameters Антипина Александра
- [AMBER] calculating absolute binding free energy using MMPBSA menwer momo
- Re: [AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10 Hannes Loeffler
- [AMBER] principal axes error using cpptraj Asmita Gupta
- Re: [AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10 Thomas Evangelidis
- Re: [AMBER] MTKPP installation error Jason Swails
- Re: [AMBER] GAFFlipid parameters Dickson, Callum J
- Re: [AMBER] MTKPP installation error Kshatresh Dutta Dubey
- Re: [AMBER] calculating absolute binding free energy using MMPBSA Jason Swails
- [AMBER] Isopeptide bond Asp-Lys - parameters? Anselm Horn
- Re: [AMBER] Ligand movement in protein cavatiy Jurgens de Bruin
- Re: [AMBER] GAFFlipid parameters Антипина Александра
- Re: [AMBER] MMPBSA error zahra khatti
- Re: [AMBER] GAFFlipid parameters Dickson, Callum J
- Re: [AMBER] Ligand movement in protein cavatiy Jason Swails
- Re: [AMBER] Ligand movement in protein cavatiy Jurgens de Bruin
- Re: [AMBER] GAFFlipid parameters Aldo Segura
- Re: [AMBER] MMPBSA error Jason Swails
- Re: [AMBER] principal axes error using cpptraj Daniel Roe
- Re: [AMBER] Parametrization of the protein with the assigned protonation states James Starlight
- Re: [AMBER] donor and acceptor group in hbond Daniel Roe
- Re: [AMBER] image distances newamber list
- Re: [AMBER] Parametrization of the protein with the assigned protonation states Jason Swails
- [AMBER] RDF Plot zahra khatti
- [AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1. mish
- [AMBER] Fw: RDF Plot zahra khatti
- Re: [AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1. Daniel Roe
- [AMBER] Analysis of CHARMM DNA trajectory using nastruct Geoffrey Gray
- Re: [AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1. mish
- Re: [AMBER] RDF Plot Jason Swails
- Re: [AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1. Daniel Roe
- Re: [AMBER] MMPBSA error Ray Luo, Ph.D.
- Re: [AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1. Daniel Roe
- Re: [AMBER] image distances Daniel Roe
- Re: [AMBER] MMPBSA error zahra khatti
- Re: [AMBER] Analysis of CHARMM DNA trajectory using nastruct Daniel Roe
- Re: [AMBER] Analysis of CHARMM DNA trajectory using nastruct Geoffrey Gray
- Re: [AMBER] calculating absolute binding free energy using MMPBSA David A Case
- Re: [AMBER] Analysis of CHARMM DNA trajectory using nastruct Jason Swails
- Re: [AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10 Benjamin D Madej
- Re: [AMBER] GAFFlipid parameters Benjamin D Madej
- Re: [AMBER] Isopeptide bond Asp-Lys - parameters? FyD
Thursday, 5 June 2014
- Re: [AMBER] MMPBSA error zahra khatti
- [AMBER] VMD and binary trajectories James Starlight
- [AMBER] On the choosing of coordinate for the umbrella sampling James Starlight
- Re: [AMBER] VMD and binary trajectories Jason Swails
- Re: [AMBER] On the choosing of coordinate for the umbrella sampling Jason Swails
- Re: [AMBER] sudden and rapid configuration change in NVT simulation yjlee
- Re: [AMBER] sudden and rapid configuration change in NVT simulation Jason Swails
- Re: [AMBER] On the choosing of coordinate for the umbrella sampling Brian Radak
- Re: [AMBER] VMD and binary trajectories James Starlight
- Re: [AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1. mish
- Re: [AMBER] On the choosing of coordinate for the umbrella sampling Carlos Simmerling
- Re: [AMBER] MMPBSA error Ray Luo, Ph.D.
- Re: [AMBER] Simulation of the protein with internal water Bill Ross
- [AMBER] error in hbond analysis Arunima Shilpi
Friday, 6 June 2014
- [AMBER] 【amber】center of mass&umbrella sampling whb
- [AMBER] Constant surface tension on the membrane James Starlight
- [AMBER] Density Plot Jurgens de Bruin
- [AMBER] cpptraj error : not parsing mdvel file Himanshu Joshi
- Re: [AMBER] error in hbond analysis Jason Swails
- Re: [AMBER] 【amber】center of mass&umbrella sampling Jason Swails
- Re: [AMBER] Density Plot Jason Swails
- Re: [AMBER] Constant surface tension on the membrane Jason Swails
- Re: [AMBER] MMPBSA error zahra khatti
- Re: [AMBER] sudden and rapid configuration change in NVT simulation yjlee
- Re: [AMBER] cpptraj error : not parsing mdvel file Daniel Roe
- Re: [AMBER] 【amber】center of mass&umbrella sampling Daniel Roe
- [AMBER] charmmlipid2amber.py James Starlight
- Re: [AMBER] charmmlipid2amber.py James Starlight
- [AMBER] Problem using charmmlipid2amber.py with VMD wmsmith.uci.edu
- [AMBER] error in hydrogen bond Arunima Shilpi
Saturday, 7 June 2014
- Re: [AMBER] error in hydrogen bond Jason Swails
- Re: [AMBER] cpptraj error : not parsing mdvel file Himanshu Joshi
- Re: [AMBER] error in hydrogen bond Soumendranath Bhakat
- [AMBER] Question about how a charged system can be simulated using PBC? yuandandan05.gmail.com
Sunday, 8 June 2014
- Re: [AMBER] Problem using charmmlipid2amber.py with VMD James Starlight
- Re: [AMBER] Question about how a charged system can be simulated using PBC? Dr. Vitaly Chaban
- [AMBER] hbond analysis Arunima Shilpi
- [AMBER] Hbond analysi Arunima Shilpi
- Re: [AMBER] Question about how a charged system can be simulated using PBC? yuandandan05.gmail.com
- Re: [AMBER] Question about how a charged system can be simulated using PBC? Jason Swails
- Re: [AMBER] Hbond analysi Daniel Roe
Monday, 9 June 2014
- [AMBER] NVT equilibration crash using CUDA James Starlight
- Re: [AMBER] NVT equilibration crash using CUDA James Starlight
- Re: [AMBER] NVT equilibration crash using CUDA Soumendranath Bhakat
- [AMBER] problem during add ions Sohag Biswas
- Re: [AMBER] NVT equilibration crash using CUDA James Starlight
- [AMBER] Fwd: Substrate moving out of the box during MD simulation-- reg Rajeswari A.
- [AMBER] [Amber 14] multi-GPU calculation error occers when specify eight GPUs with Tesla K20Xm Keisuke Aono
- Re: [AMBER] problem during add ions David A Case
- [AMBER] Is it possible to tleap a protein molecule without adding terminal atoms? #YIP YEW MUN#
- Re: [AMBER] NVT equilibration crash using CUDA Jason Swails
- Re: [AMBER] Fwd: Substrate moving out of the box during MD simulation-- reg Jason Swails
- Re: [AMBER] Is it possible to tleap a protein molecule without adding terminal atoms? Jason Swails
- Re: [AMBER] [Amber 14] multi-GPU calculation error occers when specify eight GPUs with Tesla K20Xm Ross Walker
- Re: [AMBER] problem during add ions Parvesh Singh
- Re: [AMBER] NVT equilibration crash using CUDA James Starlight
- Re: [AMBER] NVT equilibration crash using CUDA Jason Swails
- Re: [AMBER] [Amber 14] multi-GPU calculation error occers when specify eight GPUs with Tesla K20Xm Scott Le Grand
- Re: [AMBER] Is it possible to tleap a protein molecule without adding terminal atoms? Ray Luo, Ph.D.
- Re: [AMBER] NVT equilibration crash using CUDA James Starlight
- Re: [AMBER] Constant surface tension on the membrane Benjamin D Madej
- Re: [AMBER] charmmlipid2amber.py Benjamin D Madej
- Re: [AMBER] Problem using charmmlipid2amber.py with VMD Benjamin D Madej
- Re: [AMBER] charmmlipid2amber.py James Starlight
- Re: [AMBER] Problem using charmmlipid2amber.py with VMD Benjamin D Madej
- Re: [AMBER] Constant surface tension on the membrane James Starlight
- [AMBER] zlib issues during compilation. Harris, Danni
- Re: [AMBER] Problem using charmmlipid2amber.py with VMD Thomas Evangelidis
- Re: [AMBER] zlib issues during compilation. Daniel Roe
- Re: [AMBER] charmmlipid2amber.py Benjamin D Madej
- Re: [AMBER] Constant surface tension on the membrane Benjamin D Madej
- Re: [AMBER] zlib issues during compilation. Harris, Danni
- Re: [AMBER] Problem using charmmlipid2amber.py with VMD Benjamin D Madej
- Re: [AMBER] zlib issues during compilation. Daniel Roe
- Re: [AMBER] charmmlipid2amber.py James Starlight
- Re: [AMBER] charmmlipid2amber.py James Starlight
Tuesday, 10 June 2014
- [AMBER] Equilibration of membrane protein James Starlight
- [AMBER] Query about GPU model Indrajit Deb
- Re: [AMBER] NVT equilibration crash using CUDA James Starlight
- Re: [AMBER] zlib issues during compilation. Harris, Danni
- Re: [AMBER] NVT equilibration crash using CUDA Jason Swails
- Re: [AMBER] NVT equilibration crash using CUDA Daniel Roe
- [AMBER] error in using pmemd Valentina Romano
- Re: [AMBER] error in using pmemd Jason Swails
- [AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py Senthil Natesan
- Re: [AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py Jason Swails
- Re: [AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py Senthil Natesan
- [AMBER] Membrane protein tutorial James Starlight
- Re: [AMBER] charmmlipid2amber.py James Starlight
- Re: [AMBER] Membrane protein tutorial Brian Radak
- Re: [AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py Jason Swails
- Re: [AMBER] Query about GPU model Ross Walker
- Re: [AMBER] Membrane protein tutorial Jason Swails
- Re: [AMBER] Membrane protein tutorial Brian Radak
- Re: [AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py Jason Swails
- [AMBER] Side chain and backbone-specific parameters. Lee-Ping Wang
- Re: [AMBER] Query about GPU model Scott Le Grand
- Re: [AMBER] Side chain and backbone-specific parameters. Jason Swails
- Re: [AMBER] Membrane protein tutorial Jason Swails
- Re: [AMBER] Side chain and backbone-specific parameters. Lee-Ping Wang
- Re: [AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py Senthil Natesan
- Re: [AMBER] Side chain and backbone-specific parameters. Jason Swails
- Re: [AMBER] Membrane protein tutorial James Starlight
- Re: [AMBER] Side chain and backbone-specific parameters. Lee-Ping Wang
- Re: [AMBER] charmmlipid2amber.py Benjamin D Madej
- Re: [AMBER] charmmlipid2amber.py James Starlight
- Re: [AMBER] Equilibration of membrane protein Benjamin D Madej
- Re: [AMBER] Side chain and backbone-specific parameters. Jason Swails
- Re: [AMBER] charmmlipid2amber.py Benjamin D Madej
- Re: [AMBER] Query about GPU model Indrajit Deb
- Re: [AMBER] charmmlipid2amber.py James Starlight
- Re: [AMBER] MMPBSA error Ray Luo, Ph.D.
- Re: [AMBER] charmmlipid2amber.py Benjamin D Madej
- Re: [AMBER] charmmlipid2amber.py Bill Ross
- Re: [AMBER] Equilibration of membrane protein James Starlight
- Re: [AMBER] charmmlipid2amber.py James Starlight
- Re: [AMBER] charmmlipid2amber.py James Starlight
Wednesday, 11 June 2014
- Re: [AMBER] charmmlipid2amber.py James Starlight
- [AMBER] restarting MDs generated in Amber10 with Amber12 Silvia Bonomo
- Re: [AMBER] GAFFlipid parameters Alexandra Antipina
- Re: [AMBER] GAFFlipid parameters Dickson, Callum J
- Re: [AMBER] restarting MDs generated in Amber10 with Amber12 David A Case
- [AMBER] QM/MMPBSA John Smith
- Re: [AMBER] QM/MMPBSA Jason Swails
- Re: [AMBER] QM/MMPBSA John Smith
- Re: [AMBER] QM/MMPBSA Brian Radak
- Re: [AMBER] QM/MMPBSA Jason Swails
- Re: [AMBER] QM/MMPBSA John Smith
- Re: [AMBER] QM/MMPBSA Jason Swails
- [AMBER] Metal Center Parameter Builder (MCPB) manual Senthil Natesan
- [AMBER] GLYCAM parameter ATOM TYPE Soumendranath Bhakat
- Re: [AMBER] GLYCAM parameter ATOM TYPE Lachele Foley
- Re: [AMBER] charmmlipid2amber.py Benjamin D Madej
- [AMBER] Metal Center Parameter Builder (MCPB) manual Senthil Natesan
- Re: [AMBER] charmmlipid2amber.py James Starlight
Thursday, 12 June 2014
- [AMBER] MMPBSA huge VDW values maryam azimzadehirani
- Re: [AMBER] GLYCAM parameter ATOM TYPE Soumendranath Bhakat
- [AMBER] Magnesium FATAL error Soumendranath Bhakat
- Re: [AMBER] Magnesium FATAL error David A Case
- Re: [AMBER] MMPBSA huge VDW values Jason Swails
- Re: [AMBER] MMPBSA huge VDW values maryam azimzadehirani
- [AMBER] Adding residue in two end of DNA mehdi bagherpoor
- Re: [AMBER] Metal Center Parameter Builder (MCPB) manual Jason Swails
- Re: [AMBER] Metal Center Parameter Builder (MCPB) manual Senthil Natesan
- Re: [AMBER] Metal Center Parameter Builder (MCPB) manual Senthil Natesan
- [AMBER] "Invalid start to time: 28..." error Vu Truong
- Re: [AMBER] charmmlipid2amber.py Benjamin D Madej
- Re: [AMBER] charmmlipid2amber.py James Starlight
- Re: [AMBER] "Invalid start to time: 28..." error Daniel Roe
- Re: [AMBER] "Invalid start to time: 28..." error David A Case
- Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems David A Case
- Re: [AMBER] "Invalid start to time: 28..." error Bill Ross
- Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Keiran Rowell
- Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Ross Walker
Friday, 13 June 2014
- [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Kshatresh Dutta Dubey
- Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Gerald Monard
- Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Kshatresh Dutta Dubey
- Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Jason Swails
- Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Soumendranath Bhakat
- Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Kshatresh Dutta Dubey
- Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Kshatresh Dutta Dubey
- Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Soumendranath Bhakat
- Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Soumendranath Bhakat
- Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Kshatresh Dutta Dubey
- Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Soumendranath Bhakat
- [AMBER] different number of waters newamber list
- Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Gerald Monard
- Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Kshatresh Dutta Dubey
- [AMBER] Rmsd with reference structure having different number of total atoms Rajeswari A.
- Re: [AMBER] Rmsd with reference structure having different number of total atoms Rajeswari A.
- Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Kshatresh Dutta Dubey
- Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface David A Case
- Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Gerald Monard
- Re: [AMBER] Loop refirement James Starlight
- Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Kshatresh Dutta Dubey
- Re: [AMBER] "Invalid start to time: 28..." error Vu Truong
- Re: [AMBER] "Invalid start to time: 28..." error Jason Swails
- Re: [AMBER] "Invalid start to time: 28..." error Bill Ross
- [AMBER] Integration scheme used in Amber 9 and 11 ? Ravi Tripathi
Saturday, 14 June 2014
- [AMBER] The linkage of Amber and Gaussian in Amber 14. Jinfeng Huang
- Re: [AMBER] Integration scheme used in Amber 9 and 11 ? Kshatresh Dutta Dubey
- Re: [AMBER] The linkage of Amber and Gaussian in Amber 14. Jason Swails
- Re: [AMBER] Integration scheme used in Amber 9 and 11 ? Jason Swails
- Re: [AMBER] Integration scheme used in Amber 9 and 11 ? Kshatresh Dutta Dubey
- Re: [AMBER] Adding residue in two end of DNA FyD
- Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems Daniel Roe
- Re: [AMBER] "Invalid start to time: 28..." error Daniel Roe
- [AMBER] Deleting Box info from trajectory Kshatresh Dutta Dubey
- Re: [AMBER] Loop refirement James Starlight
- Re: [AMBER] Deleting Box info from trajectory David A Case
- Re: [AMBER] Deleting Box info from trajectory Daniel Roe
- Re: [AMBER] Deleting Box info from trajectory Kshatresh Dutta Dubey
- Re: [AMBER] different number of waters MURAT OZTURK
- Re: [AMBER] Deleting Box info from trajectory David A Case
- Re: [AMBER] Deleting Box info from trajectory Kshatresh Dutta Dubey
- Re: [AMBER] Deleting Box info from trajectory Jason Swails
- Re: [AMBER] different number of waters Jason Swails
- [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 余青芬
Sunday, 15 June 2014
- Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 Gerald Monard
- Re: [AMBER] Deleting Box info from trajectory Kshatresh Dutta Dubey
- Re: [AMBER] different number of waters newamber list
- Re: [AMBER] different number of waters newamber list
- Re: [AMBER] different number of waters David A Case
- Re: [AMBER] Integration scheme used in Amber 9 and 11 ? Ravi Tripathi
Monday, 16 June 2014
- Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 余青芬
- [AMBER] Topology issue with MMPBSA.py JPB
- Re: [AMBER] Topology issue with MMPBSA.py Jason Swails
- Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 Gerald Monard
- [AMBER] fitting of atomic structures to cryo-em maps Asmita Gupta
- Re: [AMBER] fitting of atomic structures to cryo-em maps Jason Swails
- Re: [AMBER] fitting of atomic structures to cryo-em maps Asmita Gupta
- Re: [AMBER] Topology issue with MMPBSA.py JPB
- Re: [AMBER] Topology issue with MMPBSA.py Jason Swails
- Re: [AMBER] fitting of atomic structures to cryo-em maps Jason Swails
- [AMBER] bash scripting for MD tasks James Starlight
- Re: [AMBER] bash scripting for MD tasks Daniel Roe
Tuesday, 17 June 2014
- [AMBER] GLYCAM_06 reference Chinthaka Ratnaweera
- Re: [AMBER] GLYCAM_06 reference Lachele Foley
- [AMBER] Glycophosphate parametrization using GLYCAM Raj Schneider
- Re: [AMBER] Glycophosphate parametrization using GLYCAM Lachele Foley
- Re: [AMBER] bash scripting for MD tasks James Starlight
- Re: [AMBER] bash scripting for MD tasks Lachele Foley
- Re: [AMBER] bash scripting for MD tasks Jason Swails
- Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems Guqin Shi
- Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems Guqin Shi
- [AMBER] cpptraj hbond - warning message Mahendra B Thapa
- Re: [AMBER] Glycophosphate parametrization using GLYCAM FyD
- [AMBER] Queries about QM/MM Tanmoy Paul
Wednesday, 18 June 2014
- Re: [AMBER] Glycophosphate parametrization using GLYCAM Jochen Heil
- Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 余青芬
- Re: [AMBER] Queries about QM/MM Jason Swails
- Re: [AMBER] Queries about QM/MM David A Case
- Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 David A Case
- Re: [AMBER] different number of waters newamber list
- Re: [AMBER] Queries about QM/MM Brian Radak
- Re: [AMBER] different number of waters Brian Radak
- Re: [AMBER] different number of waters newamber list
- Re: [AMBER] different number of waters David A Case
- Re: [AMBER] different number of waters Brian Radak
- Re: [AMBER] cpptraj hbond - warning message Jason Swails
- [AMBER] Setting up z-constraint Ylenia Cau
- Re: [AMBER] Setting up z-constraint Brian Radak
- Re: [AMBER] Setting up z-constraint Pierpaolo Cacciotto
- [AMBER] Leapfrog algorithm zahra khatti
- [AMBER] MPI and parallel installation Simone Fulle
- Re: [AMBER] Glycophosphate parametrization using GLYCAM Lachele Foley
- Re: [AMBER] Leapfrog algorithm Jason Swails
- Re: [AMBER] Glycophosphate parametrization using GLYCAM Thomas Pochapsky
- Re: [AMBER] Glycophosphate parametrization using GLYCAM Thomas Pochapsky
- [AMBER] EAMBER (non-restraint) in sander output Duggan, Brendan
- [AMBER] torsion restraint violation reporting Duggan, Brendan
- Re: [AMBER] MPI and parallel installation Gerald Monard
- Re: [AMBER] MPI and parallel installation Jason Swails
- Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 Gerald Monard
- Re: [AMBER] Leapfrog algorithm David A Case
- [AMBER] MMPBSA - calculating energy decomposition by residue in a trajectory without a ligand Andrew.Warden.csiro.au
- Re: [AMBER] MMPBSA - calculating energy decomposition by residue in a trajectory without a ligand Bill Miller III
- [AMBER] remd whb
- Re: [AMBER] EAMBER (non-restraint) in sander output David A Case
Thursday, 19 June 2014
- Re: [AMBER] Glycophosphate parametrization using GLYCAM FyD
- Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 余青芬
- Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 Gerald Monard
- Re: [AMBER] Glycophosphate parametrization using GLYCAM Jochen Heil
- Re: [AMBER] bash scripting for MD tasks James Starlight
- [AMBER] Se atom type Krisztina Feher
- Re: [AMBER] Glycophosphate parametrization using GLYCAM Lachele Foley
- [AMBER] Se atom type Krisztina Feher
- [AMBER] Derive charge of multiple molecules sunita gupta
- Re: [AMBER] Derive charge of multiple molecules Jason Swails
- [AMBER] Hi Him Shweta
- Re: [AMBER] remd Daniel Roe
- Re: [AMBER] Hi Daniel Roe
- Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems Daniel Roe
- Re: [AMBER] Topology issue with MMPBSA.py Daniel Roe
- Re: [AMBER] EAMBER (non-restraint) in sander output Duggan, Brendan
- Re: [AMBER] Setting up z-constraint Benjamin D Madej
Friday, 20 June 2014
- [AMBER] AmberTools14 installation zahra khatti
- Re: [AMBER] Glycophosphate parametrization using GLYCAM FyD
- Re: [AMBER] AmberTools14 installation Gerald Monard
- Re: [AMBER] Setting up z-constraint Pierpaolo Cacciotto
- Re: [AMBER] bash scripting for MD tasks James Starlight
- [AMBER] On the usage of the position restrains during equilibration James Starlight
- Re: [AMBER] bash scripting for MD tasks Daniel Roe
- Re: [AMBER] MMPBSA error zahra khatti
- Re: [AMBER] On the usage of the position restrains during equilibration Bill Ross
- Re: [AMBER] Setting up z-constraint Ross Walker
- Re: [AMBER] Setting up z-constraint Scott Le Grand
- Re: [AMBER] Setting up z-constraint Scott Le Grand
- Re: [AMBER] On the usage of the position restrains during equilibration James Starlight
- [AMBER] metal ion parameterisation problem Kshatresh Dutta Dubey
- Re: [AMBER] On the usage of the position restrains during equilibration Bill Ross
- Re: [AMBER] On the usage of the position restrains during equilibration Bill Ross
- Re: [AMBER] On the usage of the position restrains during equilibration James Starlight
- Re: [AMBER] Derive charge of multiple molecules sunita gupta
Saturday, 21 June 2014
- [AMBER] Se atom type Krisztina Feher
- [AMBER] segmentation_fault_loading_pdb in tleap Shomesankar Bhunia
- Re: [AMBER] segmentation_fault_loading_pdb in tleap Soumendranath Bhakat
- Re: [AMBER] segmentation_fault_loading_pdb in tleap Shomesankar Bhunia
- Re: [AMBER] Derive charge of multiple molecules Daniel Roe
- [AMBER] filter trajectory with modes same number of frames newamber list
- [AMBER] MTK++ Error Kshatresh Dutta Dubey
- Re: [AMBER] filter trajectory with modes same number of frames Daniel Roe
- Re: [AMBER] MTK++ Error Kshatresh Dutta Dubey
- Re: [AMBER] filter trajectory with modes same number of frames newamber list
- Re: [AMBER] Se atom type Jason Swails
Sunday, 22 June 2014
- Re: [AMBER] bash scripting for MD tasks James Starlight
- Re: [AMBER] Derive charge of multiple molecules Soumendranath Bhakat
- Re: [AMBER] Derive charge of multiple molecules Soumendranath Bhakat
- Re: [AMBER] bash scripting for MD tasks Parker de Waal
- Re: [AMBER] bash scripting for MD tasks Parker de Waal
- [AMBER] AMBER 12 Nucleic Acid Builder (NAB) language loue chen
- Re: [AMBER] On the usage of the position restrains during equilibration Jason Swails
- Re: [AMBER] metal ion parameterisation problem Ben Roberts
Monday, 23 June 2014
- [AMBER] MM/PBSA calculation. Him Shweta
- Re: [AMBER] Setting up z-constraint Pierpaolo Cacciotto
- [AMBER] Low performance in multi-pmemd.mpi James Starlight
- Re: [AMBER] Se atom type Krisztina Feher
- Re: [AMBER] bash scripting for MD tasks James Starlight
- [AMBER] tleap using GLYCAM force field Shreeramesh
- Re: [AMBER] Se atom type David A Case
- [AMBER] Condensed Glycam notation for gammacyclodextrin Shreeramesh
- Re: [AMBER] MM/PBSA calculation. Jason Swails
- [AMBER] Clustering using CPPTRAJ Soumendranath Bhakat
- Re: [AMBER] Low performance in multi-pmemd.mpi Daniel Roe
- Re: [AMBER] Clustering using CPPTRAJ Daniel Roe
- Re: [AMBER] Clustering using CPPTRAJ Soumendranath Bhakat
- Re: [AMBER] metal ion parameterisation problem Ken Merz
- Re: [AMBER] bash scripting for MD tasks Parker de Waal
- Re: [AMBER] Clustering using CPPTRAJ Soumendranath Bhakat
- Re: [AMBER] metal ion parameterisation problem Kshatresh Dutta Dubey
- Re: [AMBER] Setting up z-constraint Ross Walker
- Re: [AMBER] Clustering using CPPTRAJ Jason Swails
- Re: [AMBER] tleap using GLYCAM force field Lachele Foley
- [AMBER] Some error in output file and restart kirtana S
- Re: [AMBER] Some error in output file and restart Jason Swails
- Re: [AMBER] MM/PBSA calculation. Him Shweta
- Re: [AMBER] Condensed Glycam notation for gammacyclodextrin Lachele Foley
- Re: [AMBER] metal ion parameterisation problem Pengfei Li
- Re: [AMBER] MM/PBSA calculation. Jason Swails
- Re: [AMBER] Clustering using CPPTRAJ Soumendranath Bhakat
- Re: [AMBER] Clustering using CPPTRAJ Jason Swails
- [AMBER] Query about parallel GPU multijob Kshatresh Dutta Dubey
- Re: [AMBER] metal ion parameterisation problem Kshatresh Dutta Dubey
- Re: [AMBER] Query about parallel GPU multijob Ross Walker
- Re: [AMBER] Some error in output file and restart Ross Walker
- Re: [AMBER] Query about parallel GPU multijob Kshatresh Dutta Dubey
- Re: [AMBER] Query about parallel GPU multijob Kshatresh Dutta Dubey
- Re: [AMBER] Query about parallel GPU multijob Ross Walker
- Re: [AMBER] Query about parallel GPU multijob Kshatresh Dutta Dubey
- Re: [AMBER] Query about parallel GPU multijob Ross Walker
- Re: [AMBER] Query about parallel GPU multijob Kshatresh Dutta Dubey
- Re: [AMBER] MMPBSA - calculating energy decomposition by residue in a trajectory without a ligand Andrew.Warden.csiro.au
- Re: [AMBER] Query about parallel GPU multijob Ross Walker
- Re: [AMBER] Query about parallel GPU multijob Kshatresh Dutta Dubey
- Re: [AMBER] Some error in output file and restart kirtana S
- Re: [AMBER] MM/PBSA calculation. Him Shweta
Tuesday, 24 June 2014
- [AMBER] Force field for carbohydrates-Reg. Shreeramesh
- [AMBER] Sirius executable not available anymore? Felix Terwesten
- Re: [AMBER] Sirius executable not available anymore? David A Case
- [AMBER] about setting iwrap kirtana S
- [AMBER] tleap for gammacyclodextrin-Reg. Shreeramesh
- Re: [AMBER] about setting iwrap Daniel Roe
- Re: [AMBER] filter trajectory with modes same number of frames Daniel Roe
- Re: [AMBER] Some error in output file and restart Ross Walker
- Re: [AMBER] tleap for gammacyclodextrin-Reg. Lachele Foley
- Re: [AMBER] tleap for gammacyclodextrin-Reg. Lachele Foley
- Re: [AMBER] Sirius executable not available anymore? Ross Walker
- [AMBER] Amber scaling on culster George Tzotzos
- Re: [AMBER] Amber scaling on culster Roitberg,Adrian E
- Re: [AMBER] Amber scaling on culster Ross Walker
- Re: [AMBER] Amber scaling on culster Ross Walker
- Re: [AMBER] filter trajectory with modes same number of frames newamber list
- [AMBER] Problem in creating prmtop inpcrd file in leap 肖立
- Re: [AMBER] Problem in creating prmtop inpcrd file in leap Bill Ross
- Re: [AMBER] Problem in creating prmtop inpcrd file in leap David A Case
- [AMBER] Issues in .out trying to simulat a polymer in AMBER Andrew.Warden.csiro.au
Wednesday, 25 June 2014
- Re: [AMBER] Issues in .out trying to simulat a polymer in AMBER David A Case
Tuesday, 24 June 2014
- Re: [AMBER] Force field for carbohydrates-Reg. FyD
Wednesday, 25 June 2014
- Re: [AMBER] Amber scaling on culster George Tzotzos
- Re: [AMBER] Force field for carbohydrates-Reg. Lachele Foley
- Re: [AMBER] Force field for carbohydrates-Reg. Lachele Foley
- Re: [AMBER] Problem in creating prmtop inpcrd file in leap 肖立
- Re: [AMBER] metal ion parameterisation problem Pengfei Li
- [AMBER] Issues in .out trying to simulat a polymer in AMBER Andrew.Warden.csiro.au
- [AMBER] simulation differences in pmemd.MPI and pmemd.cuda Manikanthan Bhavaraju
- Re: [AMBER] simulation differences in pmemd.MPI and pmemd.cuda Soumendranath Bhakat
- Re: [AMBER] simulation differences in pmemd.MPI and pmemd.cuda Ross Walker
- Re: [AMBER] simulation differences in pmemd.MPI and pmemd.cuda Manikanthan Bhavaraju
Thursday, 26 June 2014
- Re: [AMBER] Sirius executable not available anymore? Felix Terwesten
- Re: [AMBER] Sirius executable not available anymore? David A Case
- [AMBER] Fwd: problem while USING GLYCAM for Gammacyclodextrin-Reg. Shreeramesh
- [AMBER] Torsional profile of butane Yingjie Wang
- Re: [AMBER] Fwd: problem while USING GLYCAM for Gammacyclodextrin-Reg. Lachele Foley
- Re: [AMBER] Torsional profile of butane Jason Swails
- Re: [AMBER] Torsional profile of butane Yingjie Wang
- [AMBER] 3D-RISM: charge density, charge distribution, and electrostatic potential Brian Radak
- Re: [AMBER] Torsional profile of butane Jason Swails
- [AMBER] periodic box drifted during NVE run Quynh Vo
- Re: [AMBER] Torsional profile of butane FyD
Friday, 27 June 2014
- [AMBER] formal charge of the ligand Mary Varughese
- Re: [AMBER] formal charge of the ligand Jason Swails
- Re: [AMBER] formal charge of the ligand Soumendranath Bhakat
- Re: [AMBER] formal charge of the ligand Jason Swails
- [AMBER] Analyze properties of in parallel MD Valentina Romano
- Re: [AMBER] Torsional profile of butane Yingjie Wang
- Re: [AMBER] Analyze properties of in parallel MD Brian Radak
- [AMBER] No VDWAALS EEL in PB MMPBSA.py job JPB
- Re: [AMBER] Analyze properties of in parallel MD Jason Swails
- Re: [AMBER] formal charge of the ligand Soumendranath Bhakat
- Re: [AMBER] No VDWAALS EEL in PB MMPBSA.py job Ray Luo, Ph.D.
- Re: [AMBER] 3D-RISM: charge density, charge distribution, and electrostatic potential T Luchko (Lists)
- [AMBER] Per residue rmsd Chinthaka Ratnaweera
- Re: [AMBER] Per residue rmsd Soumendranath Bhakat
- Re: [AMBER] Per residue rmsd Chinthaka Ratnaweera
- Re: [AMBER] Per residue rmsd Jason Swails
- Re: [AMBER] Per residue rmsd Soumendranath Bhakat
- Re: [AMBER] Per residue rmsd Daniel Roe
- [AMBER] Printing out matrix labels Eugene Yedvabny
- Re: [AMBER] Printing out matrix labels Daniel Roe
- Re: [AMBER] formal charge of the ligand Mary Varughese
Saturday, 28 June 2014
- Re: [AMBER] periodic box drifted during NVE run David A Case
- [AMBER] QMMM NEB reaction pathway calculation with AMBER Teerapong Pirojsirikul
Sunday, 29 June 2014
- Re: [AMBER] QMMM NEB reaction pathway calculation with AMBER Jason Swails
- Re: [AMBER] Printing out matrix labels Eugene Yedvabny
- Re: [AMBER] Printing out matrix labels Eugene Yedvabny
Monday, 30 June 2014
- [AMBER] Early termination of parallel MD Valentina Romano
- Re: [AMBER] Early termination of parallel MD Anna Bauß
- Re: [AMBER] Early termination of parallel MD Valentina Romano
- Re: [AMBER] Early termination of parallel MD Anselm Horn
- [AMBER] Efficient, accurate estimation of relative binding free energies Guo, Zhuyan
- Re: [AMBER] Efficient, accurate estimation of relative binding free energies Jason Swails
- Re: [AMBER] Early termination of parallel MD Jason Swails
- Re: [AMBER] Printing out matrix labels Jason Swails
- Re: [AMBER] Printing out matrix labels Daniel Roe
- [AMBER] cpptraj: arithmetic on data sets? Brian Radak
- Re: [AMBER] Falling apart of membrane Gözde YALÇIN
- Re: [AMBER] QMMM NEB reaction pathway calculation with AMBER Teerapong Pirojsirikul
- Re: [AMBER] Falling apart of membrane Benjamin D Madej

Last message date: Mon Jun 30 2014 - 14:30:02 PDT
Archived on: Fri Nov 15 2024 - 05:55:02 PST

Amber Archive Jun 2014 by date