Amber Archive Nov 2015: by date

Saturday, 31 October 2015
- Re: [AMBER] ions cannot be viewed in gaussview Martina Devi
- [AMBER] MM-PBSA quasi harmonic Debodyuti Dutta
Sunday, 1 November 2015
- Re: [AMBER] &rst + distance + coordinate restraint Jason Swails
- Re: [AMBER] MM-PBSA quasi harmonic Jason Swails
- Re: [AMBER] ions cannot be viewed in gaussview Martina Devi
- Re: [AMBER] ions cannot be viewed in gaussview Robert Molt
- Re: [AMBER] Can't install AMBER14: MissingProgram...Install patch from your package manager Jose Borreguero
- Re: [AMBER] ions cannot be viewed in gaussview Gustavo Seabra
- Re: [AMBER] ions cannot be viewed in gaussview Martina Devi
- Re: [AMBER] ions cannot be viewed in gaussview Jason Swails
- Re: [AMBER] ions cannot be viewed in gaussview Gustavo Seabra
- Re: [AMBER] ions cannot be viewed in gaussview MOHD HOMAIDUR RAHMAN
Monday, 2 November 2015
- Re: [AMBER] (too) high absolute values for charges using resp and gaussian Jérémie Knoops
- [AMBER] Tutorial A26: error in reading nameless control Ruth Helena Tichauer
- [AMBER] How comment in mdin sander input file? Alan
- Re: [AMBER] How comment in mdin sander input file? Eiros Zamora, Juan
- [AMBER] rMD || Distance-Restrained Molecular Dynamics Refinement in Explicit Solvent (AMBER) -- SCRIPT V. Kumar
- Re: [AMBER] Tutorial A26: error in reading nameless control David A Case
- Re: [AMBER] rMD || Distance-Restrained Molecular Dynamics Refinement in Explicit Solvent (AMBER) -- SCRIPT Carlos Simmerling
- Re: [AMBER] How comment in mdin sander input file? David A Case
- [AMBER] Fwd: Regarding QM/MM calculation in AMBER14 Sivanandam M
- [AMBER] How to add restraints to a ligand correctly while decoupling it from complex? wliu
- Re: [AMBER] How comment in mdin sander input file? Alan
- Re: [AMBER] (too) high absolute values for charges using resp and gaussian Jérémie Knoops
- Re: [AMBER] ions cannot be viewed in gaussview Martina Devi
- Re: [AMBER] Tutorial 22 - aMD - how long should it last on Titan Black? Karolina Markowska
- Re: [AMBER] ions cannot be viewed in gaussview Jason Swails
- Re: [AMBER] Fwd: Regarding QM/MM calculation in AMBER14 Adrian Roitberg
- Re: [AMBER] Fwd: Regarding QM/MM calculation in AMBER14 Jason Swails
- Re: [AMBER] Fwd: Regarding QM/MM calculation in AMBER14 David A Case
- Re: [AMBER] ions cannot be viewed in gaussview David A Case
- Re: [AMBER] ions cannot be viewed in gaussview Aleksandra Skoric
- Re: [AMBER] Tutorial A26: error in reading nameless control Ruth Helena Tichauer
- Re: [AMBER] Tutorial A26: error in reading nameless control Jason Swails
- Re: [AMBER] Tutorial A26: error in reading nameless control Ruth Helena Tichauer
- [AMBER] decomp bad atom type: fe Abelak, Kavin
- Re: [AMBER] rMD || Distance-Restrained Molecular Dynamics Refinement in Explicit Solvent (AMBER) -- SCRIPT V. Kumar
- Re: [AMBER] ions cannot be viewed in gaussview Daniel Roe
- Re: [AMBER] (too) high absolute values for charges using resp and gaussian Karl Kirschner
- Re: [AMBER] ions cannot be viewed in gaussview Martina Devi
- Re: [AMBER] ions cannot be viewed in gaussview Jason Swails
- Re: [AMBER] rMD || Distance-Restrained Molecular Dynamics Refinement in Explicit Solvent (AMBER) -- SCRIPT Jason Swails
- Re: [AMBER] &rst + distance + coordinate restraint Daniel Roe
- Re: [AMBER] ions cannot be viewed in gaussview Martina Devi
- Re: [AMBER] rMD || Distance-Restrained Molecular Dynamics Refinement in Explicit Solvent (AMBER) -- SCRIPT V. Kumar
- Re: [AMBER] ions cannot be viewed in gaussview Jason Swails
- [AMBER] trajout our mask pdb with connection records windy
- [AMBER] trajout or mask pdb with connection records (title is wrong, see this one) windy
Tuesday, 3 November 2015
- [AMBER] Entropy can be neglecected under which condition Marc Zhang
- Re: [AMBER] Entropy can be neglecected under which condition sunita gupta
- [AMBER] ff14SB acetylated residues Neha Gandhi
- Re: [AMBER] ff14SB acetylated residues Carlos Simmerling
- Re: [AMBER] Entropy can be neglecected under which condition Carlos Simmerling
- Re: [AMBER] trajout or mask pdb with connection records (title is wrong, see this one) Jason Swails
- Re: [AMBER] Entropy can be neglecected under which condition Marc Zhang
- Re: [AMBER] How to add restraints to a ligand correctly while decoupling it from complex? Jason Swails
- Re: [AMBER] &rst + distance + coordinate restraint Gerald Monard
- Re: [AMBER] &rst + distance + coordinate restraint Jason Swails
- Re: [AMBER] &rst + distance + coordinate restraint Gerald Monard
- [AMBER] ncorr in rotdif command seems redundant to me. Please help. Jose Borreguero
- Re: [AMBER] ncorr in rotdif command seems redundant to me. Please help. case
- Re: [AMBER] ncorr in rotdif command seems redundant to me. Please help. Daniel Roe
Wednesday, 4 November 2015
- [AMBER] How to choose between implicit and explicit solvent Jean-Patrick Francoia
- Re: [AMBER] How to choose between implicit and explicit solvent Carlos Simmerling
- Re: [AMBER] ncorr in rotdif command seems redundant to me. Please help. Jose Borreguero
- Re: [AMBER] ncorr in rotdif command seems redundant to me. Please help. David A Case
- Re: [AMBER] How to choose between implicit and explicit solvent Jean-Patrick Francoia
- Re: [AMBER] How to choose between implicit and explicit solvent Carlos Simmerling
- [AMBER] What to expect when MD a peptide and a small organic molecule ? Jean-Patrick Francoia
- Re: [AMBER] How to choose between implicit and explicit solvent Jean-Patrick Francoia
- Re: [AMBER] What to expect when MD a peptide and a small organic molecule ? Jason Swails
- Re: [AMBER] How to choose between implicit and explicit solvent Jason Swails
- Re: [AMBER] How to choose between implicit and explicit solvent Carlos Simmerling
- [AMBER] Center of mass restraints with pmemd.cuda abdennour braka
- Re: [AMBER] Center of mass restraints with pmemd.cuda Kevin Hauser
- Re: [AMBER] Center of mass restraints with pmemd.cuda abdennour braka
- Re: [AMBER] Center of mass restraints with pmemd.cuda Jason Swails
- Re: [AMBER] How to choose between implicit and explicit solvent Fabian gmail
- Re: [AMBER] How to choose between implicit and explicit solvent David A Case
- [AMBER] Gaussian Accelerated Molecular Dynamics Filip Fratev
- Re: [AMBER] Gaussian Accelerated Molecular Dynamics Ross Walker
- Re: [AMBER] Gaussian Accelerated Molecular Dynamics Albert
- Re: [AMBER] Gaussian Accelerated Molecular Dynamics Jason Swails
- Re: [AMBER] Gaussian Accelerated Molecular Dynamics Filip Fratev
- Re: [AMBER] Gaussian Accelerated Molecular Dynamics Ross Walker
- [AMBER] AMBER14 cuda installation problem Sanjib Paul
- Re: [AMBER] trajout or mask pdb with connection records (title is wrong, see this one) windy
- Re: [AMBER] AMBER14 cuda installation problem Charles Lin
- Re: [AMBER] AMBER14 cuda installation problem Charles Lin
Thursday, 5 November 2015
- [AMBER] orientational restraints in MD simulation Naomi Rose Latorraca
- Re: [AMBER] How to choose between implicit and explicit solvent Fabian gmail
- Re: [AMBER] What to expect when MD a peptide and a small organic molecule ? Jean-Patrick Francoia
- Re: [AMBER] How to choose between implicit and explicit solvent Jean-Patrick Francoia
- Re: [AMBER] AMBER14 cuda installation problem Sanjib Paul
- Re: [AMBER] What to expect when MD a peptide and a small organic molecule ? Carlos Simmerling
- Re: [AMBER] How to choose between implicit and explicit solvent David A Case
- Re: [AMBER] How to choose between implicit and explicit solvent Fabian gmail
- Re: [AMBER] trajout or mask pdb with connection records (title is wrong, see this one) Daniel Roe
- [AMBER] ptraj and cpptraj 袁浩亮
- Re: [AMBER] ptraj and cpptraj Jason Swails
- [AMBER] NMR restraints + minimization+Could not find cntrl namelist V. Kumar
- Re: [AMBER] NMR restraints + minimization+Could not find cntrl namelist Carlos Simmerling
- Re: [AMBER] NMR restraints + minimization+Could not find cntrl namelist V. Kumar
- [AMBER] MMPBSA.py QM entropy calculation error Nic Steussy
- Re: [AMBER] NMR restraints + minimization+Could not find cntrl namelist David A Case
- Re: [AMBER] NMR restraints + minimization+Could not find cntrl namelist V. Kumar
- [AMBER] Cpptraj Tutorial B1 Aishani Prem
- Re: [AMBER] Cpptraj Tutorial B1 V. Kumar
- Re: [AMBER] Cpptraj Tutorial B1 Daniel Roe
- Re: [AMBER] Cpptraj Tutorial B1 Aishani Prem
- Re: [AMBER] Cpptraj Tutorial B1 Aishani Prem
- Re: [AMBER] MMPBSA.py QM entropy calculation error Jason Swails
- Re: [AMBER] MMPBSA.py QM entropy calculation error Daniel Roe
Friday, 6 November 2015
- Re: [AMBER] What to expect when MD a peptide and a small organic molecule ? Jean-Patrick Francoia
- [AMBER] power failure + resume shahab shariati
- Re: [AMBER] power failure + resume Daniel Roe
- Re: [AMBER] power failure + resume shahab shariati
- [AMBER] Convert namd input file into sander input format? Xing
- Re: [AMBER] Convert namd input file into sander input format? Jason Swails
- Re: [AMBER] power failure + resume Jason Swails
Sunday, 8 November 2015
- [AMBER] make complex Fatemeh Sadat Alavi
- Re: [AMBER] power failure + resume shahab shariati
- Re: [AMBER] power failure + resume shahab shariati
- Re: [AMBER] power failure + resume Bill
- Re: [AMBER] power failure + resume Bill
- Re: [AMBER] power failure + resume Jason Swails
- Re: [AMBER] make complex case
- [AMBER] NOE calculation cpptraj Neha Gandhi
- [AMBER] How to solve the unfilled valence problem in antechamber 张敏华
- [AMBER] PLUMED patching with AMBER Sanjib Paul
- Re: [AMBER] PLUMED patching with AMBER Giovanni Bussi
Monday, 9 November 2015
- Re: [AMBER] make complex Fatemeh Sadat Alavi
- Re: [AMBER] make complex Jason Swails
- Re: [AMBER] NOE calculation cpptraj Jason Swails
- Re: [AMBER] NOE calculation cpptraj David A Case
- Re: [AMBER] How to solve the unfilled valence problem in antechamber David A Case
- Re: [AMBER] make complex David A Case
- Re: [AMBER] QM/MM Umbrella Mahmood Jasim
- Re: [AMBER] QM/MM Umbrella Adrian Roitberg
- [AMBER] A query about distance between periodic images anu chandra
- Re: [AMBER] How to choose between implicit and explicit solvent Josh Berryman
- Re: [AMBER] How to choose between implicit and explicit solvent Ross Walker
- [AMBER] can't install MMPBSA.py.MPI 情生太郎
- Re: [AMBER] can't install MMPBSA.py.MPI Hai Nguyen
- Re: [AMBER] can't install MMPBSA.py.MPI case
- Re: [AMBER] NOE calculation cpptraj Neha Gandhi
- [AMBER] Role of VDWAALS and EEL in minimization muhammad tahir ayub
- Re: [AMBER] How to choose between implicit and explicit solvent Josh Berryman
Tuesday, 10 November 2015
- [AMBER] GIST Yulian Gavrilov
- [AMBER] neighbouring protons Neha Gandhi
- Re: [AMBER] Role of VDWAALS and EEL in minimization Carlos Simmerling
- Re: [AMBER] neighbouring protons Jason Swails
- Re: [AMBER] GIST Steven Ramsey
- Re: [AMBER] GIST Jonathan Gough
Wednesday, 11 November 2015
- [AMBER] Stability calculations from MMGB/PBSA Rajeswari A.
- Re: [AMBER] N- and C- terminals constant PH simulation Hadeer ELHabashy
- [AMBER] Problem with MMPBSA Soong Jiaxin
- Re: [AMBER] Problem with MMPBSA Bill
- Re: [AMBER] Problem with MMPBSA Soong Jiaxin
- [AMBER] High Positive Values of delta G in MMPBSA Hira Jabeen
- [AMBER] Sampling of membrane-protein system Ofir Tal
- [AMBER] High Positive Values of delta G in MMPBSA Hira Jabeen
- Re: [AMBER] GIST Yulian Gavrilov
- Re: [AMBER] N- and C- terminals constant PH simulation Carlos Simmerling
- Re: [AMBER] Stability calculations from MMGB/PBSA Carlos Simmerling
- [AMBER] Few queries about simulation of protein - carbohydrate system anu chandra
- Re: [AMBER] Problem with MMPBSA Jason Swails
- Re: [AMBER] Stability calculations from MMGB/PBSA David A Case
- Re: [AMBER] Sampling of membrane-protein system Jason Swails
- Re: [AMBER] High Positive Values of delta G in MMPBSA Jason Swails
- Re: [AMBER] cpptraj uses huge memory space while doing molsurf calculation anu chandra
- Re: [AMBER] Problem with MMPBSA Soong Jiaxin
- Re: [AMBER] N- and C- terminals constant PH simulation Jason Swails
- Re: [AMBER] Problem with MMPBSA Jason Swails
- Re: [AMBER] Stability calculations from MMGB/PBSA Jason Swails
- Re: [AMBER] Sampling of membrane-protein system Ofir Tal
- Re: [AMBER] Problem with MMPBSA Soong Jiaxin
- Re: [AMBER] cpptraj uses huge memory space while doing molsurf calculation David A Case
- Re: [AMBER] Sampling of membrane-protein system Brian Radak
- [AMBER] MMPBSA Electrostatic energy Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] GIST Steven Ramsey
- Re: [AMBER] MMPBSA Electrostatic energy Jason Swails
- Re: [AMBER] MMPBSA Electrostatic energy Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] MMPBSA Electrostatic energy Jason Swails
- Re: [AMBER] MMPBSA Electrostatic energy Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] MMPBSA Electrostatic energy Jason Swails
- Re: [AMBER] MMPBSA Electrostatic energy asma.msbi28.iiu.edu.pk
- Re: [AMBER] Stability calculations from MMGB/PBSA Rajeswari A.
Thursday, 12 November 2015
- [AMBER] For atom: .R<Na+ 264>.A<Na+ 1> Could not find vdW (or other) parameters for type: IP Sumra Wajid Abbasi 30-FBAS/MSBI/F09
- Re: [AMBER] GIST Yulian Gavrilov
- Re: [AMBER] Stability calculations from MMGB/PBSA Andrea Spitaleri
- Re: [AMBER] For atom: .R<Na+ 264>.A<Na+ 1> Could not find vdW (or other) parameters for type: IP Bill
- Re: [AMBER] PLUMED patching with AMBER Sanjib Paul
- Re: [AMBER] PLUMED patching with AMBER Giovanni Bussi
- Re: [AMBER] Polardecomp in 3D-RISM fails Josep Maria Campanera Alsina
- Re: [AMBER] For atom: .R<Na+ 264>.A<Na+ 1> Could not find vdW (or other) parameters for type: IP David A Case
- Re: [AMBER] PLUMED patching with AMBER Jason Swails
- Re: [AMBER] Polardecomp in 3D-RISM fails Jason Swails
- [AMBER] Questions about TI lipengfei_mail
- Re: [AMBER] PLUMED patching with AMBER Giovanni Bussi
- [AMBER] how to create a 20% or 30% acetone / water equilibrated solvent box Fabian gmail
- Re: [AMBER] PLUMED patching with AMBER Jason Swails
- [AMBER] GPU run fails Fabian gmail
- [AMBER] Simulating Inifinite DNA molecules Balaji Selvam
- Re: [AMBER] Simulating Inifinite DNA molecules Ilyas Yildirim
- Re: [AMBER] GPU run fails Jason Swails
- Re: [AMBER] GPU run fails Ross Walker
- [AMBER] Gpu info Carlos Romero
- Re: [AMBER] Gpu info Ross Walker
- Re: [AMBER] Simulating Inifinite DNA molecules Jason Swails
- Re: [AMBER] how to create a 20% or 30% acetone / water equilibrated solvent box David A Case
- Re: [AMBER] Gpu info Carlos Romero
- [AMBER] add support 4 file format antechamber Sofia Vasilakaki
- Re: [AMBER] Gpu info Scott Le Grand
- Re: [AMBER] Gpu info Carlos Romero
Friday, 13 November 2015
- [AMBER] Lipid14 simulation :MC Barostat vs Berendsen Barostat and NTR=1 Himanshu Joshi
- Re: [AMBER] Lipid14 simulation :MC Barostat vs Berendsen Barostat and NTR=1 Himanshu Joshi
- Re: [AMBER] PLUMED patching with AMBER Sanjib Paul
- Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal
- Re: [AMBER] Few queries about simulation of protein - carbohydrate system David A Case
- Re: [AMBER] add support 4 file format antechamber David A Case
- Re: [AMBER] Few queries about simulation of protein - carbohydrate system aneesh cna
- [AMBER] Saving trajectories with ntwprt Batuhan Kav
- Re: [AMBER] Saving trajectories with ntwprt Jason Swails
- Re: [AMBER] Combined cartesian and NMR restraints Peter Podbevšek
- [AMBER] relaxation time CphMD Arjun Sharma
- Re: [AMBER] PLUMED patching with AMBER Giovanni Bussi
- Re: [AMBER] relaxation time CphMD Brian Radak
- Re: [AMBER] relaxation time CphMD Jason Swails
- Re: [AMBER] Lipid14 simulation :MC Barostat vs Berendsen Barostat and NTR=1 Ross Walker
- Re: [AMBER] Lipid14 simulation :MC Barostat vs Berendsen Barostat and NTR=1 Himanshu Joshi
- Re: [AMBER] Lipid14 simulation :MC Barostat vs Berendsen Barostat and NTR=1 Jason Swails
- [AMBER] error with NMA calculation Mohammad Salem
- Re: [AMBER] error with NMA calculation Jason Swails
- Re: [AMBER] For atom: .R<Na+ 264>.A<Na+ 1> Could not find vdW (or other) parameters for type: IP Sumra Wajid Abbasi 30-FBAS/MSBI/F09
Saturday, 14 November 2015
- [AMBER] how to plot a graph for enthalpy ayesha afzaal
- Re: [AMBER] how to plot a graph for enthalpy Jason Swails
- Re: [AMBER] PLUMED patching with AMBER Sanjib Paul
- [AMBER] query for plotting enthalpy graph Ayesha Kanwal
- Re: [AMBER] query for plotting enthalpy graph Jason Swails
- Re: [AMBER] how to plot a graph for enthalpy Ayesha Kanwal
- Re: [AMBER] how to plot a graph for enthalpy Ayesha Kanwal
- Re: [AMBER] how to plot a graph for enthalpy asma.msbi28.iiu.edu.pk
- Re: [AMBER] how to plot a graph for enthalpy Jason Swails
- Re: [AMBER] PLUMED patching with AMBER Giovanni Bussi
- Re: [AMBER] how to plot a graph for enthalpy Jason Swails
- Re: [AMBER] Positive delta G in MM-PBSA Jason Swails
- Re: [AMBER] how to plot a graph for enthalpy psu4.uic.edu
- Re: [AMBER] how to plot a graph for enthalpy Ayesha Kanwal
- Re: [AMBER] Problem with MMPBSA psu4.uic.edu
Sunday, 15 November 2015
- Re: [AMBER] GPU run fails Fabian gmail
- Re: [AMBER] how to create a 20% or 30% acetone / water equilibrated solvent box Fabian gmail
- Re: [AMBER] PLUMED patching with AMBER Sanjib Paul
Monday, 16 November 2015
- [AMBER] mono methylated lysine Bala subramanian
- Re: [AMBER] Few queries about simulation of protein - carbohydrate system Lachele Foley
- Re: [AMBER] error with NMA calculation Mohammad
- Re: [AMBER] mono methylated lysine Sourav Purohit
Tuesday, 17 November 2015
- Re: [AMBER] error with NMA calculation David A Case
- [AMBER] temperature control issue during constant pH simulation with explicit solvent model zhonghe xu
- Re: [AMBER] temperature control issue during constant pH simulation with explicit solvent model Carlos Simmerling
- Re: [AMBER] temperature control issue during constant pH simulation with explicit solvent model Jason Swails
- Re: [AMBER] Few queries about simulation of protein - carbohydrate system anu chandra
- [AMBER] free energy of solvation of small molecules Fabian gmail
- Re: [AMBER] free energy of solvation of small molecules Hannes Loeffler
- [AMBER] Making .mdl files for 1DRISM calculations Ella Gale
- Re: [AMBER] free energy of solvation of small molecules Fabian gmail
- Re: [AMBER] free energy of solvation of small molecules Hannes Loeffler
- Re: [AMBER] free energy of solvation of small molecules Fabian gmail
- Re: [AMBER] Making .mdl files for 1DRISM calculations Tyler Luchko (Lists)
- [AMBER] Typo or My Confusion Robert Molt
- [AMBER] Typo or My Confusion Robert Molt
- [AMBER] net charge issue during constant pH simulation with explicit solvent model zhonghe xu
Wednesday, 18 November 2015
- Re: [AMBER] Questions about TI psu4.uic.edu
- [AMBER] Number of water molecule to solvate 2.5KDa peptide in TIP3PBOX V. Kumar
- Re: [AMBER] "Vlimit exceeded for step..." error Vishnudatt Pandey
- Re: [AMBER] Questions about TI hannes.loeffler.stfc.ac.uk
- [AMBER] Backbone mohammad roostaie
- [AMBER] Backbone mohammad r
- [AMBER] Backbone mohammad r
- Re: [AMBER] Backbone Karl Kirschner
- Re: [AMBER] Making .mdl files for 1DRISM calculations Ella Gale
- Re: [AMBER] Backbone mohammad r
- Re: [AMBER] Typo or My Confusion David A Case
- Re: [AMBER] Backbone Jason Swails
- Re: [AMBER] Number of water molecule to solvate 2.5KDa peptide in TIP3PBOX David A Case
- Re: [AMBER] Number of water molecule to solvate 2.5KDa peptide in TIP3PBOX V. Kumar
- Re: [AMBER] Backbone Daniel Roe
- Re: [AMBER] Typo or My Confusion Robert Molt
- Re: [AMBER] Backbone mohammad r
- Re: [AMBER] Typo or My Confusion Jason Swails
- Re: [AMBER] "Vlimit exceeded for step..." error Jason Swails
- Re: [AMBER] net charge issue during constant pH simulation with explicit solvent model Jason Swails
- Re: [AMBER] Making .mdl files for 1DRISM calculations Tyler Luchko (Lists)
- Re: [AMBER] Making .mdl files for 1DRISM calculations David A Case
- Re: [AMBER] Backbone David A Case
- Re: [AMBER] Backbone mohammad r
- Re: [AMBER] error with NMA calculation Mohammad Salem
- [AMBER] urea force field Carlos Romero
- Re: [AMBER] error with NMA calculation Jason Swails
- [AMBER] (no subject) Facebook
- Re: [AMBER] urea force field Karl Kirschner
Thursday, 19 November 2015
- [AMBER] Distorted and Failed Phosphate Simulations Sigurd Friis Truelsen
- Re: [AMBER] Distorted and Failed Phosphate Simulations Karl Kirschner
- [AMBER] cpptraj grid command Thomas Fox
- Re: [AMBER] error with NMA calculation David A Case
- Re: [AMBER] Distorted and Failed Phosphate Simulations pavel.banas.upol.cz
- Re: [AMBER] Distorted and Failed Phosphate Simulations David A Case
- [AMBER] Putting a harmonic constraint between atoms Debodyuti Dutta
- Re: [AMBER] Putting a harmonic constraint between atoms Jason Swails
- Re: [AMBER] urea force field Carlos Romero
- Re: [AMBER] urea force field Jason Swails
- Re: [AMBER] Typo or My Confusion Ross Walker
- [AMBER] decomposition energy Fabian gmail
- Re: [AMBER] free energy of solvation of small molecules Fabian gmail
- Re: [AMBER] cpptraj grid command Daniel Roe
- Re: [AMBER] free energy of solvation of small molecules Hannes Loeffler
- Re: [AMBER] cpptraj grid command Thomas Fox
- Re: [AMBER] decomposition energy Jason Swails
- [AMBER] Error compiling amber14 with CUDA-7.0 (CentOS 7) Elvis Martis
- Re: [AMBER] query for plotting enthalpy graph Ayesha Kanwal
Friday, 20 November 2015
- Re: [AMBER] Distorted and Failed Phosphate Simulations Karl Kirschner
- [AMBER] (no subject) Facebook
- Re: [AMBER] query for plotting enthalpy graph David A Case
- Re: [AMBER] Error compiling amber14 with CUDA-7.0 (CentOS 7) Jason Swails
- [AMBER] units of charge density Ignacio J. General
- [AMBER] (no subject) Facebook
- [AMBER] (no subject) Facebook
- Re: [AMBER] urea force field Carlos Romero
- Re: [AMBER] cpptraj grid command Daniel Roe
- Re: [AMBER] Error compiling amber14 with CUDA-7.0 (CentOS 7) Elvis Martis
Saturday, 21 November 2015
- Re: [AMBER] Error compiling amber14 with CUDA-7.0 (CentOS 7) Sofia Vasilakaki
- Re: [AMBER] Error compiling amber14 with CUDA-7.0 (CentOS 7) Jason Swails
- [AMBER] cpptraj density command Ignacio J. General
- Re: [AMBER] cpptraj density command David A Case
- [AMBER] 10 Lowest energy structures from GB ==>Explicit solvent refinement V. Kumar
- Re: [AMBER] cpptraj density command Daniel Roe
- Re: [AMBER] 10 Lowest energy structures from GB ==>Explicit solvent refinement David A Case
- [AMBER] Apologize Carlos Romero
- Re: [AMBER] Error compiling amber14 with CUDA-7.0 (CentOS 7) Elvis Martis
Sunday, 22 November 2015
- Re: [AMBER] 10 Lowest energy structures from GB ==>Explicit solvent refinement V. Kumar
- Re: [AMBER] cpptraj density command Ignacio J. General
- [AMBER] QMMM: ERROR! Ayesha Kanwal
- Re: [AMBER] QMMM: ERROR! Ross Walker
- Re: [AMBER] free energy of solvation of small molecules Josh Berryman
Monday, 23 November 2015
- [AMBER] Can LEaP create peptides with D-amino acids? Yip Yew Mun
- Re: [AMBER] QMMM: ERROR! Ayesha Kanwal
- Re: [AMBER] Can LEaP create peptides with D-amino acids? Carlos Simmerling
- Re: [AMBER] Can LEaP create peptides with D-amino acids? Marion, Antoine
- Re: [AMBER] QMMM: ERROR! Ayesha Kanwal
- Re: [AMBER] QMMM: ERROR! Jason Swails
- Re: [AMBER] Can LEaP create peptides with D-amino acids? Carlos Simmerling
- Re: [AMBER] free energy of solvation of small molecules Fabian gmail
- Re: [AMBER] How to fix the QM/MM region box size and visualize it Sivanandam M
- Re: [AMBER] QMMM: ERROR! David A Case
- Re: [AMBER] How to fix the QM/MM region box size and visualize it Gustavo Seabra
- [AMBER] MD simulation for multiple ligands Balajee Ramachandran
- [AMBER] how to add lipid mohammad r
- [AMBER] how to add lipid mohammad r
- Re: [AMBER] how to add lipid Brian Radak
- Re: [AMBER] how to add lipid mohammad r
- Re: [AMBER] how to add lipid Brian Radak
- Re: [AMBER] how to add lipid Parker de Waal
- Re: [AMBER] how to add lipid mohammad r
- Re: [AMBER] how to add lipid Parker de Waal
- Re: [AMBER] how to add lipid mohammad r
- [AMBER] Running simulations in a cluster Aishani Prem
- Re: [AMBER] Running simulations in a cluster Jason Swails
- Re: [AMBER] MD simulation for multiple ligands Jason Swails
Tuesday, 24 November 2015
- [AMBER] query about Br Ayesha Kanwal
- Re: [AMBER] Distorted and Failed Phosphate Simulations Sigurd Friis Truelsen
- [AMBER] Protein-Drug complex MD simulation issues Vahid Kshani
- Re: [AMBER] Protein-Drug complex MD simulation issues Bill
- Re: [AMBER] query about Br Ayesha Kanwal
- [AMBER] (no subject) Facebook
- Re: [AMBER] Distorted and Failed Phosphate Simulations Jason Swails
- [AMBER] (no subject) Facebook
- Re: [AMBER] query about Br David A Case
- [AMBER] MMGBSA Decomp on Heme Systems Vivek Bharadwaj
- Re: [AMBER] MMGBSA Decomp on Heme Systems Jason Swails
- [AMBER] Import error when running MMPBSA.py Cockroft, Nicholas T.
- [AMBER] NAB nmode() output Clarification Guqin Shi
- Re: [AMBER] Import error when running MMPBSA.py Dwight McGee
- Re: [AMBER] Import error when running MMPBSA.py Cockroft, Nicholas T.
- Re: [AMBER] Import error when running MMPBSA.py Nhai
- Re: [AMBER] Import error when running MMPBSA.py Hai Nguyen
- Re: [AMBER] Import error when running MMPBSA.py Dwight McGee
- [AMBER] iwrap=1 "can mess up diffusion and other calculations" Robert Molt
- Re: [AMBER] iwrap=1 "can mess up diffusion and other calculations" Charles Lin
- Re: [AMBER] iwrap=1 "can mess up diffusion and other calculations" Jason Swails
- Re: [AMBER] iwrap=1 "can mess up diffusion and other calculations" Robert Molt
- Re: [AMBER] iwrap=1 "can mess up diffusion and other calculations" Jason Swails
Wednesday, 25 November 2015
- [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics jinfeng liu
- Re: [AMBER] cpptraj grid command Thomas Fox
- Re: [AMBER] free energy of solvation of small molecules Fabian gmail
- Re: [AMBER] free energy of solvation of small molecules Hannes Loeffler
- Re: [AMBER] free energy of solvation of small molecules Fabian gmail
- Re: [AMBER] free energy of solvation of small molecules Hannes Loeffler
- Re: [AMBER] free energy of solvation of small molecules Fabian gmail
- Re: [AMBER] free energy of solvation of small molecules hannes.loeffler.stfc.ac.uk
- Re: [AMBER] NAB nmode() output Clarification David A Case
- Re: [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics David A Case
- Re: [AMBER] free energy of solvation of small molecules Fabian gmail
- Re: [AMBER] NAB nmode() output Clarification Guqin Shi
- Re: [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics jinfeng liu
- Re: [AMBER] free energy of solvation of small molecules Hannes Loeffler
- Re: [AMBER] free energy of solvation of small molecules Fabian gmail
- [AMBER] Deformed structures Damiano Spadoni
- Re: [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics Daniel Roe
- Re: [AMBER] MMGBSA Decomp on Heme Systems Vivek Bharadwaj
- Re: [AMBER] Import error when running MMPBSA.py Cockroft, Nicholas T.
- Re: [AMBER] Deformed structures David A Case
- Re: [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics jinfeng liu
Thursday, 26 November 2015
- Re: [AMBER] Deformed structures Damiano Spadoni
- Re: [AMBER] cpptraj grid command Daniel Roe
- [AMBER] At line 434 of file make_crd_hg.F (unit = 5, file = 'stdin') Fortran runtime error: Bad value during floating point read. leila karami
- Re: [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics David A Case
- Re: [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics David A Case
- Re: [AMBER] At line 434 of file make_crd_hg.F (unit = 5, file = 'stdin') Fortran runtime error: Bad value during floating point read. leila karami
- Re: [AMBER] At line 434 of file make_crd_hg.F (unit = 5, file = 'stdin') Fortran runtime error: Bad value during floating point read. David A Case
- Re: [AMBER] At line 434 of file make_crd_hg.F (unit = 5, file = 'stdin') Fortran runtime error: Bad value during floating point read. Bill
- Re: [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics jinfeng liu
Friday, 27 November 2015
- [AMBER] Error message while running alanine dipeptide tutorial (minimization) Nikolay N. Kuzmich
- Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) Bill
- [AMBER] Fwd: Replica exchange problem in visualization and interpretation of the MD out files maryam azimzadehirani
- [AMBER] Adding parameters to the force field Timofey Tyugashev
- Re: [AMBER] Fwd: Replica exchange problem in visualization and interpretation of the MD out files Carlos Simmerling
- Re: [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics David A Case
- Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) David A Case
Sunday, 29 November 2015
- Re: [AMBER] free energy of solvation of small molecules Fabian gmail
- Re: [AMBER] free energy of solvation of small molecules Fabian gmail
- [AMBER] MMPBSA Balajee Ramachandran
- Re: [AMBER] MMPBSA David A Case
- Re: [AMBER] Adding parameters to the force field David A Case
- [AMBER] Not matching test AMBER14 with CUDA Mijiddorj Batsaikhan
- Re: [AMBER] Not matching test AMBER14 with CUDA Ross Walker
Monday, 30 November 2015
- Re: [AMBER] free energy of solvation of small molecules hannes.loeffler.stfc.ac.uk
- Re: [AMBER] free energy of solvation of small molecules Fabian gmail
- Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) Nikolay N. Kuzmich
- Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) Carlos Simmerling
- [AMBER] How to fix malloc error during MM-PBSA calculation on AMBER14 ... mmpbsa_py_energy: malloc.c:2372: sysmalloc: Mijiddorj Batsaikhan
- [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond V. Kumar
- Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond Carlos Simmerling
- Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond V. Kumar
- Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond Pengfei Li
- Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond Carlos Simmerling
- Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) Bill
- Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) David A Case
- Re: [AMBER] mac hangs when compile ambertools15 on El capitan Hai Nguyen

Last message date: Mon Nov 30 2015 - 21:00:02 PST
Archived on: Mon Nov 03 2025 - 05:55:15 PST

Amber Archive Nov 2015 by date