Amber Archive Nov 2017: by date

Wednesday, 1 November 2017
- [AMBER] PB Bomb in pb_aaradi() while running mmpbsa.py Urszula Uciechowska
- [AMBER] pulling along RMSD Qinghua Liao
- [AMBER] protein && DNA in implicit solvents Qinghua Liao
- Re: [AMBER] protein && DNA in implicit solvents Carlos Simmerling
- [AMBER] the best APS is not zero, bonds involved by this atom are frozen Shilpa Gupta
- [AMBER] energy minimum vs binding pose for charge calculation Thomas Evangelidis
- Re: [AMBER] energy minimum vs binding pose for charge calculation David A Case
- Re: [AMBER] energy minimum vs binding pose for charge calculation Thomas Evangelidis
- [AMBER] MCPB.py step 1 help please Eugene Cha
- Re: [AMBER] the best APS is not zero, bonds involved by this atom are frozen David A Case
- Re: [AMBER] protein && DNA in implicit solvents Qinghua Liao
- Re: [AMBER] energy minimum vs binding pose for charge calculation Thomas Evangelidis
- [AMBER] How to generate inpcrd and prmtop files for A and B mixed solution 杨满意
Thursday, 2 November 2017
- [AMBER] Miniconda gives error while compiling AmberTools-17 Biplab Ghosh
- Re: [AMBER] How to generate inpcrd and prmtop files for A and B mixed solution David A Case
- Re: [AMBER] Miniconda gives error while compiling AmberTools-17 Hai Nguyen
- Re: [AMBER] How to generate inpcrd and prmtop files for A and B mixed solution 杨满意
- Re: [AMBER] How to generate inpcrd and prmtop files for A and B mixed solution David A Case
- Re: [AMBER] How to generate inpcrd and prmtop files for A and B mixed solution 杨满意
- [AMBER] Acetate ion using xleap Shilpa Gupta
- Re: [AMBER] Acetate ion using xleap Bill Ross
- Re: [AMBER] Acetate ion using xleap Shilpa Gupta
- Re: [AMBER] Acetate ion using xleap Bill Ross
- Re: [AMBER] Acetate ion using xleap Shilpa Gupta
- Re: [AMBER] Acetate ion using xleap Bill Ross
Friday, 3 November 2017
- [AMBER] mmpbsa.py error Urszula Uciechowska
- [AMBER] chloride as anion Shilpa Gupta
- Re: [AMBER] chloride as anion Carlos Simmerling
- Re: [AMBER] chloride as anion Shilpa Gupta
- [AMBER] H-REMD Dr. MANAS MONDAL
- Re: [AMBER] mmpbsa.py error Ray Luo
- [AMBER] 1-4 scaling factors in case of GAFF-GLYCAM mixed dihedral terms ? Marek Maly
- Re: [AMBER] problem with TUTORAL C5: Hydrogen Bond Analysis with CPPTRAJ Rodrigo Galindo-Murillo
- Re: [AMBER] problem with TUTORAL C5: Hydrogen Bond Analysis with CPPTRAJ Setyanto Md
- Re: [AMBER] H-REMD Feng Pan
- Re: [AMBER] H-REMD Dr. MANAS MONDAL
- Re: [AMBER] H-REMD Feng Pan
Saturday, 4 November 2017
- [AMBER] Automatic rotation of the protein by LEAP to minimize the periodic cell dimensions? Dmitry Suplatov
- Re: [AMBER] Automatic rotation of the protein by LEAP to minimize the periodic cell dimensions? Bill Ross
- Re: [AMBER] 1-4 scaling factors in case of GAFF-GLYCAM mixed dihedral terms ? Lachele Foley
- [AMBER] Distance restrain usage for fixing distance between two atoms jacob wick
- Re: [AMBER] 1-4 scaling factors in case of GAFF-GLYCAM mixed dihedral terms ? Marek Maly
Sunday, 5 November 2017
- Re: [AMBER] 1-4 scaling factors in case of GAFF-GLYCAM mixed dihedral terms ? Lachele Foley
- Re: [AMBER] 1-4 scaling factors in case of GAFF-GLYCAM mixed dihedral terms ? Marek Maly
Monday, 6 November 2017
- Re: [AMBER] Distance restrain usage for fixing distance between two atoms David A Case
- [AMBER] Free Energy GPU Johannes Löffler
- Re: [AMBER] Free Energy GPU Ross Walker
- [AMBER] Unknown flag error - sander Mo Rahman
- Re: [AMBER] Unknown flag error - sander Hai Nguyen
- Re: [AMBER] Unknown flag error - sander Hai Nguyen
- [AMBER] Hydrogen atom SHAKEH problem sangita kachhap
- Re: [AMBER] Free Energy GPU Taisung Lee
- Re: [AMBER] Free Energy GPU Feng Pan
- Re: [AMBER] Free Energy GPU Darrin Y
- [AMBER] No Cartesian force constants found Sushi Shilpa
- [AMBER] Need information regarding frcmod.urea Saikat Pal
Tuesday, 7 November 2017
- Re: [AMBER] Wrong connectivity after antechamber/Gaussian16 Andreas Tosstorff
- [AMBER] New ligand [antechamber->prepgen->parmchk2->xLeap] Taylor, Miles
- [AMBER] change in density on multiple gpus Neha Gandhi
- [AMBER] error: Atom does not have type Shilpa Gupta
- Re: [AMBER] error: Atom does not have type Bill Ross
Wednesday, 8 November 2017
- Re: [AMBER] New ligand [antechamber->prepgen->parmchk2->xLeap] David A Case
- [AMBER] No torsion terms error even though I specified them in frcmod file Adebayo Adeniyi
- [AMBER] H-bond analysis Mustafa Alhaji Isa
- Re: [AMBER] change in density on multiple gpus Ross Walker
- Re: [AMBER] No Cartesian force constants found Pengfei Li
- Re: [AMBER] MCPB.py step 1 help please Pengfei Li
- [AMBER] Fwd: Can't load MEOHBOX as solvent Chetna Tyagi
- Re: [AMBER] H-bond analysis Daniel Roe
- Re: [AMBER] change in density on multiple gpus Neha Gandhi
- Re: [AMBER] change in density on multiple gpus Ross Walker
- Re: [AMBER] change in density on multiple gpus Neha Gandhi
- Re: [AMBER] Fwd: Can't load MEOHBOX as solvent David A Case
Thursday, 9 November 2017
- [AMBER] mmpbsa.py Urszula Uciechowska
- [AMBER] solvation box Shilpa Gupta
- Re: [AMBER] solvation box Bill Ross
- [AMBER] Computer for running MD simulation using Amber Ashok Kumar
- Re: [AMBER] Computer for running MD simulation using Amber Bill Ross
- Re: [AMBER] Computer for running MD simulation using Amber Marek Havrila
- Re: [AMBER] Fwd: Can't load MEOHBOX as solvent Chetna Tyagi
- Re: [AMBER] solvation box David A Case
- Re: [AMBER] mmpbsa.py Ray Luo
- [AMBER] Energy Calculations by cpptraj sylvester kisembo
- Re: [AMBER] Energy Calculations by cpptraj Daniel Roe
- Re: [AMBER] mmpbsa.py Urszula Uciechowska
- Re: [AMBER] mmpbsa.py Ray Luo
- Re: [AMBER] Running Explicit pH MD Pacheco, Sayuri
Friday, 10 November 2017
- [AMBER] REMD jobs slowing down unexpectedly Andreas Tosstorff
- [AMBER] UREA PDB file from xleap Saikat Pal
- Re: [AMBER] change in density on multiple gpus Ross Walker
- Re: [AMBER] UREA PDB file from xleap David A Case
- [AMBER] Is accelerated MD suitable for DFG-flip simulation in kinase? 张姝姝
- Re: [AMBER] Running Explicit pH MD Cruzeiro,Vinicius Wilian D
- [AMBER] Amber GCC 6.4.0 and MKL 2017.3.196 build failing Joachim Hein
- Re: [AMBER] Amber GCC 6.4.0 and MKL 2017.3.196 build failing Joachim Hein
- Re: [AMBER] Running Explicit pH MD Pacheco, Sayuri
- Re: [AMBER] REMD jobs slowing down unexpectedly Thomas Cheatham
- Re: [AMBER] Running Explicit pH MD Cruzeiro,Vinicius Wilian D
- Re: [AMBER] Running Explicit pH MD Pacheco, Sayuri
- Re: [AMBER] change in density on multiple gpus Neha Gandhi
- Re: [AMBER] UREA PDB file from xleap Saikat Pal
- Re: [AMBER] UREA PDB file from xleap Bill Ross
Saturday, 11 November 2017
- [AMBER] ntxo option in amber Leena Aggarwal
- Re: [AMBER] ntxo option in amber Bill Ross
- Re: [AMBER] ntxo option in amber Leena Aggarwal
- Re: [AMBER] ntxo option in amber Bill Ross
- Re: [AMBER] ntxo option in amber David A Case
- [AMBER] suggestion for a GTX 1080 ilhan.yavuz
Sunday, 12 November 2017
- [AMBER] error of pdb4amber jacky zhao
- Re: [AMBER] error of pdb4amber Hai Nguyen
- [AMBER] force field for xylose Osman, Roman
- Re: [AMBER] error of pdb4amber jacky zhao
- Re: [AMBER] force field for xylose Hector A. Baldoni
- [AMBER] the CYX problem of generation parm7 crd files by AT17 jacky zhao
- Re: [AMBER] suggestion for a GTX 1080 Ross Walker
- Re: [AMBER] error of pdb4amber Hai Nguyen
- Re: [AMBER] the CYX problem of generation parm7 crd files by AT17 Hai Nguyen
- Re: [AMBER] the CYX problem of generation parm7 crd files by AT17 Hai Nguyen
- Re: [AMBER] the CYX problem of generation parm7 crd files by AT17 Hai Nguyen
- [AMBER] error of pdb4amber Lei Zhao
- Re: [AMBER] suggestion for a GTX 1080 Scott Le Grand
Monday, 13 November 2017
- Re: [AMBER] suggestion for a GTX 1080 ilhan.yavuz
- [AMBER] cpptraj error Rana Rehan Khalid
- Re: [AMBER] cpptraj error Bill Ross
- Re: [AMBER] cpptraj error Rana Rehan Khalid
- Re: [AMBER] cpptraj error Bill Ross
- [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations Eric Lang
- [AMBER] Cross-vendor GPU layer for Machine Learning Bill Ross
- Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations Bill Ross
- Re: [AMBER] cpptraj error Rana Rehan Khalid
- Re: [AMBER] cpptraj error Bill Ross
- [AMBER] Cpptraj pdb snapshots Lizelle Lubbe
- Re: [AMBER] cpptraj error Rana Rehan Khalid
- Re: [AMBER] cpptraj error Rana Rehan Khalid
- Re: [AMBER] cpptraj error Rana Rehan Khalid
- Re: [AMBER] cpptraj error Bill Ross
- Re: [AMBER] suggestion for a GTX 1080 Ross Walker
- Re: [AMBER] cpptraj error Rana Rehan Khalid
- [AMBER] Convert prmtop Lizelle Lubbe
- Re: [AMBER] Cpptraj pdb snapshots David A Case
- Re: [AMBER] cpptraj error Rana Rehan Khalid
- Re: [AMBER] Cpptraj pdb snapshots Lizelle Lubbe
- Re: [AMBER] cpptraj error Bill Ross
- [AMBER] MMPBSA.py error: “Could not set up '_MMPBSA_receptor.mdcrd.0' for reading” Alonso Martinez, Diego
- Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations Cruzeiro,Vinicius Wilian D
- Re: [AMBER] Convert prmtop David A Case
- Re: [AMBER] Convert prmtop Lizelle Lubbe
- [AMBER] Regarding MCPB.py error Aashish Bhatt
- Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations Eric Lang
- Re: [AMBER] Regarding MCPB.py error Pengfei Li
- Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations Eric Lang
- Re: [AMBER] Regarding MCPB.py error Pengfei Li
- Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations Cruzeiro,Vinicius Wilian D
- Re: [AMBER] error of pdb4amber jacky zhao
- [AMBER] Domain domain interaction study Rana Rehan Khalid
- Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations Bill Ross
Tuesday, 14 November 2017
- [AMBER] MC barostat filip
- Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations Eric Lang
- [AMBER] pdb snapshots Lizelle Lubbe
- Re: [AMBER] pdb snapshots David A Case
- [AMBER] Regarding Glucose dynamics Aashish Bhatt
- Re: [AMBER] Regarding Glucose dynamics Lachele Foley
- Re: [AMBER] Regarding Glucose dynamics Aashish Bhatt
- Re: [AMBER] Regarding Glucose dynamics Carlos Simmerling
- Re: [AMBER] Regarding Glucose dynamics Aashish Bhatt
- [AMBER] Help Yuliia Varenyk
- Re: [AMBER] Regarding Glucose dynamics Carlos Simmerling
- Re: [AMBER] Regarding Glucose dynamics Bill Ross
- Re: [AMBER] Regarding Glucose dynamics Bill Ross
- Re: [AMBER] Regarding Glucose dynamics Aashish Bhatt
- Re: [AMBER] Regarding Glucose dynamics Lachele Foley
- [AMBER] restrain charge during MCPB.py parametrization Antonija Tomić
- Re: [AMBER] Amber GCC 6.4.0 and MKL 2017.3.196 build failing Daniel Roe
- Re: [AMBER] Help Daniel Roe
- Re: [AMBER] cpptraj error Daniel Roe
- Re: [AMBER] MC barostat Niel Henriksen
- Re: [AMBER] MC barostat David Cerutti
- Re: [AMBER] restrain charge during MCPB.py parametrization Pengfei Li
- [AMBER] The strange way of paramfit working process viktor drobot
- [AMBER] Confusion in urea Model Saikat Pal
- Re: [AMBER] restrain charge during MCPB.py parametrization Antonija Tomić
- [AMBER] Cpptraj Rana Rehan Khalid
Wednesday, 15 November 2017
- Re: [AMBER] The strange way of paramfit working process David Cerutti
- Re: [AMBER] MC barostat filip
- Re: [AMBER] MC barostat David Cerutti
- Re: [AMBER] MC barostat filip
- Re: [AMBER] The strange way of paramfit working process viktor drobot
- Re: [AMBER] pdb snapshots Lizelle Lubbe
- Re: [AMBER] Confusion in urea Model David A Case
- Re: [AMBER] Confusion in urea Model mirzo
- Re: [AMBER] The strange way of paramfit working process viktor drobot
- Re: [AMBER] Cpptraj Daniel Roe
- Re: [AMBER] pdb snapshots Daniel Roe
- [AMBER] Analysis of percentage contact in residue-ligand interaction with CPPTRAJ anu chandra
Thursday, 16 November 2017
- [AMBER] Query regarding MCPB.py force constant Abhilash J
- [AMBER] MMPBSA.py calculations on protein domain Prithvi Raj Pandey
- Re: [AMBER] Query regarding MCPB.py force constant Abhilash J
- [AMBER] PCA scree plots Lizelle Lubbe
- Re: [AMBER] PCA scree plots Lizelle Lubbe
- [AMBER] All interactions fraction analysis Ruchika Bhat
- [AMBER] Parameterizing cardiolipins in Lipid17 force field Prunotto Alessio
- [AMBER] DFTB3 Holger Kruse
- [AMBER] Distorted peptide Chetna Tyagi
- Re: [AMBER] Distorted peptide Carlos Simmerling
- [AMBER] Fw(4): sudipta.mml.gmail.com sudipta.mml
- [AMBER] simulations of enzyme with ligand Qinghua Liao
- Re: [AMBER] Running Explicit pH MD Cruzeiro,Vinicius Wilian D
- Re: [AMBER] Running Explicit pH MD Pacheco, Sayuri
- Re: [AMBER] The strange way of paramfit working process Robin Betz
- Re: [AMBER] The strange way of paramfit working process David Cerutti
- [AMBER] How to extract one frame from a trajectory to use as input file for new MD run? James Kress
- Re: [AMBER] How to extract one frame from a trajectory to use as input file for new MD run? Bill Ross
- Re: [AMBER] How to extract one frame from a trajectory to use as input file for new MD run? David A Case
- [AMBER] What does "NRF ne Abs NRFX" error (Gaussian 09) mean? Rinsha Chk
Friday, 17 November 2017
- [AMBER] MMPBSA's output: Which atoms are treated as Backbone Atoms (and Side Chain Atoms) for Nucleic Acids? Emmanuel
- [AMBER] AMBER QM/MM Point charges daniele selli
- [AMBER] Is GAFF polarizable forcefield ?? Saikat Pal
- Re: [AMBER] AMBER QM/MM Point charges Gustavo Seabra
- Re: [AMBER] Is GAFF polarizable forcefield ?? David A Case
- Re: [AMBER] AMBER QM/MM Point charges daniele selli
- Re: [AMBER] The strange way of paramfit working process viktor drobot
- Re: [AMBER] The strange way of paramfit working process David Cerutti
- Re: [AMBER] AMBER QM/MM Point charges Gustavo Seabra
- Re: [AMBER] How to extract one frame from a trajectory to use as input file for new MD run? James Kress
Saturday, 18 November 2017
- [AMBER] PCA eigenvalues Lizelle Lubbe
Sunday, 19 November 2017
- [AMBER] Fwd: simulations of enzyme with ligand Qinghua Liao
- [AMBER] Equilibration sara.iti.lk
- [AMBER] problem in minimization Carlos Romero
Monday, 20 November 2017
- Re: [AMBER] Equilibration Bill Ross
- Re: [AMBER] problem in minimization Bill Ross
- [AMBER] Query about the Glucose Parameters Aashish Bhatt
- Re: [AMBER] PCA eigenvalues Daniel Roe
- Re: [AMBER] Fwd: simulations of enzyme with ligand Daniel Roe
- Re: [AMBER] problem in minimization Carlos Romero
- Re: [AMBER] Fwd: simulations of enzyme with ligand Qinghua Liao
- [AMBER] Help Regarding Amber Tools Jerrano Bowleg
- Re: [AMBER] How to extract one frame from a trajectory to use as input file for new MD run? Daniel Roe
- Re: [AMBER] Analysis of percentage contact in residue-ligand interaction with CPPTRAJ Wesley Michael Botello-Smith
- [AMBER] Can't find pad4amber module. minyuan.mail.ustc.edu.cn
- Re: [AMBER] Analysis of percentage contact in residue-ligand interaction with CPPTRAJ anu chandra
- Re: [AMBER] Can't find pad4amber module. Hai Nguyen
- Re: [AMBER] [SPAM] Re: Can't find pad4amber module. minyuan.mail.ustc.edu.cn
Tuesday, 21 November 2017
- [AMBER] Does amber16 support gaussian16? minyuan.mail.ustc.edu.cn
- [AMBER] How to generate a cis-isomoerization of PRO? Wenbo Zhang
- [AMBER] SHAKEH problem in GPU calculation sangita kachhap
- [AMBER] SHAKEH problem in GPU calculation sangita kachhap
- Re: [AMBER] SHAKEH problem in GPU calculation David A Case
- Re: [AMBER] Analysis of percentage contact in residue-ligand interaction with CPPTRAJ Daniel Roe
- Re: [AMBER] Query about the Glucose Parameters Lachele Foley
- Re: [AMBER] Does amber16 support gaussian16? Pengfei Li
- [AMBER] 回复: Re: Does amber16 support gaussian16? 闵媛
- [AMBER] T.I. - single topology HIP <-> HIE Andrew Schaub
- Re: [AMBER] Does amber16 support gaussian16? Pengfei Li
- Re: [AMBER] Query about the Glucose Parameters Aashish Bhatt
- Re: [AMBER] Equilibration sara.iti.lk
Wednesday, 22 November 2017
- Re: [AMBER] Equilibration Bill Ross
- Re: [AMBER] Does amber16 support gaussian16? minyuan.mail.ustc.edu.cn
- [AMBER] SCEE/SCNB zeros Stefan Doerr
- Re: [AMBER] SCEE/SCNB zeros David A Case
- Re: [AMBER] SCEE/SCNB zeros Ross Walker
- Re: [AMBER] Query about the Glucose Parameters Lachele Foley
- Re: [AMBER] SCEE/SCNB zeros Stefan Doerr
- [AMBER] cpptraj: partial charges missing from mol2 file Thomas Evangelidis
- Re: [AMBER] cpptraj: partial charges missing from mol2 file Daniel Roe
- [AMBER] About position restrains Pablo Galaz-Davison
- [AMBER] how to set hetrodimer for MD Simulation Rana Rehan Khalid
- Re: [AMBER] About position restrains Thomas Cheatham
- Re: [AMBER] cpptraj: partial charges missing from mol2 file Thomas Evangelidis
- Re: [AMBER] Equilibration sara.iti.lk
- Re: [AMBER] Equilibration Bill Ross
- Re: [AMBER] Equilibration Lizelle Lubbe
Thursday, 23 November 2017
- Re: [AMBER] how to set hetrodimer for MD Simulation David A Case
- [AMBER] cudaGetDeviceCount failed unknown error Ercig Bogac (BIOCH)
- Re: [AMBER] cudaGetDeviceCount failed unknown error Ross Walker
- Re: [AMBER] cudaGetDeviceCount failed unknown error Ercig Bogac (BIOCH)
- Re: [AMBER] PCA eigenvalues Lizelle Lubbe
- Re: [AMBER] cudaGetDeviceCount failed unknown error Taisung Lee
- Re: [AMBER] cudaGetDeviceCount failed unknown error Ercig Bogac (BIOCH)
- Re: [AMBER] Equiliibration sara.iti.lk
- Re: [AMBER] Equiliibration sara.iti.lk
- Re: [AMBER] Query about the Glucose Parameters Aashish Bhatt
- [AMBER] Can we study the bond breaking event through Md simulation Rana Rehan Khalid
- Re: [AMBER] Can we study the bond breaking event through Md simulation Elvis Martis
- Re: [AMBER] Can we study the bond breaking event through Md simulation Rana Rehan Khalid
- Re: [AMBER] Can we study the bond breaking event through Md simulation Bill Ross
- Re: [AMBER] Can we study the bond breaking event through Md simulation Rana Rehan Khalid
Friday, 24 November 2017
- Re: [AMBER] Can we study the bond breaking event through Md simulation Ercig Bogac (BIOCH)
- Re: [AMBER] Can we study the bond breaking event through Md simulation Rana Rehan Khalid
- Re: [AMBER] Can we study the bond breaking event through Md simulation Szymon Żaczek
- Re: [AMBER] PCA eigenvalues Nisha Amarnath Jonniya
- Re: [AMBER] PCA eigenvalues Elvis Martis
- Re: [AMBER] Query about the Glucose Parameters David A Case
- Re: [AMBER] Query about the Glucose Parameters Lachele Foley
- Re: [AMBER] Query about the Glucose Parameters mirzo
Saturday, 25 November 2017
- Re: [AMBER] Query about the Glucose Parameters Marcelo Andrade Chagas
- Re: [AMBER] Can we study the bond breaking event through Md simulation Rana Rehan Khalid
- [AMBER] Regarding Resp charge Aashish Bhatt
- [AMBER] What forcefield does the DHFR JAC benchmark system use? John Chodera
- Re: [AMBER] cudaGetDeviceCount failed unknown error Ross Walker
- Re: [AMBER] What forcefield does the DHFR JAC benchmark system use? Ross Walker
- Re: [AMBER] What forcefield does the DHFR JAC benchmark system use? David Cerutti
- Re: [AMBER] What forcefield does the DHFR JAC benchmark system use? David Cerutti
- [AMBER] Batch Minimization Abdul-Rashid III Sampaco
- Re: [AMBER] Batch Minimization Daniel Roe
- Re: [AMBER] Batch Minimization Abdul-Rashid III Sampaco
Sunday, 26 November 2017
- [AMBER] Hydrogen bond analysis Through CPPTRAJ Rana Rehan Khalid
- Re: [AMBER] What forcefield does the DHFR JAC benchmark system use? John Chodera
- [AMBER] any opportunity of using the pmemd.cuda if one cannot afford the fee MinYuan
Monday, 27 November 2017
- Re: [AMBER] PCA eigenvalues Nisha Amarnath Jonniya
- Re: [AMBER] PCA eigenvalues Bill Ross
- Re: [AMBER] PCA eigenvalues Bill Ross
- Re: [AMBER] PCA eigenvalues Elvis Martis
- Re: [AMBER] PCA eigenvalues Nisha Amarnath Jonniya
- Re: [AMBER] any opportunity of using the pmemd.cuda if one cannot afford the fee David A Case
- Re: [AMBER] PCA eigenvalues Marcelo Andrade Chagas
- [AMBER] STOP PMEMD Terminated Abnormally MinYuan
- Re: [AMBER] PCA eigenvalues Daniel Roe
- Re: [AMBER] STOP PMEMD Terminated Abnormally Elvis Martis
- Re: [AMBER] PCA eigenvalues Daniel Roe
- Re: [AMBER] Hydrogen bond analysis Through CPPTRAJ Daniel Roe
- Re: [AMBER] cpptraj: partial charges missing from mol2 file Daniel Roe
- Re: [AMBER] Hydrogen bond analysis Through CPPTRAJ Rana Rehan Khalid
- [AMBER] Multidomain protein Simulation Rana Rehan Khalid
- Re: [AMBER] STOP PMEMD Terminated Abnormally MinYuan
- Re: [AMBER] STOP PMEMD Terminated Abnormally Hai Nguyen
- Re: [AMBER] STOP PMEMD Terminated Abnormally MinYuan
Tuesday, 28 November 2017
- Re: [AMBER] PCA eigenvalues Nisha Amarnath Jonniya
- [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib MinYuan
- Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib Bill Ross
- [AMBER] structure minimization Rana Rehan Khalid
- Re: [AMBER] structure minimization Marcelo Andrade Chagas
- Re: [AMBER] structure minimization Rana Rehan Khalid
- [AMBER] APR error Maura Malinska
- Re: [AMBER] structure minimization Bill Ross
- Re: [AMBER] structure minimization Rana Rehan Khalid
- Re: [AMBER] APR error Bill Ross
- Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib David A Case
- Re: [AMBER] structure minimization David A Case
- Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib Daniel Roe
- Re: [AMBER] structure minimization Rana Rehan Khalid
- [AMBER] Centriod in clustering sangita kachhap
- Re: [AMBER] Centriod in clustering Daniel Roe
- Re: [AMBER] Centriod in clustering sangita kachhap
- [AMBER] About PCA and pi-stacking Elisa Pieri
- [AMBER] aMD- alphaD- what does solute residues mean? Thakur, Abhishek
- Re: [AMBER] APR error Jian Yin
- Re: [AMBER] APR error Jian Yin
- Re: [AMBER] [SPAM] Re: cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib MinYuan
- Re: [AMBER] Does amber16 support gaussian16? Pengfei Li
- Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib MinYuan
- [AMBER] how to generate the force fied file of AsO3H3? minyuan.mail.ustc.edu.cn
Wednesday, 29 November 2017
- Re: [AMBER] how to generate the force fied file of AsO3H3? Bill Ross
- [AMBER] mpirun Error opening unit 5 MinYuan
- Re: [AMBER] mpirun Error opening unit 5 Bill Ross
- [AMBER] Fw: mpirun Error opening unit 5 MinYuan
- Re: [AMBER] how to generate the force fied file of AsO3H3? MinYuan
- [AMBER] Using soft-core potentials to run TI simulations Yang Jinpeng
- Re: [AMBER] PCA eigenvalues Nisha Amarnath Jonniya
- Re: [AMBER] aMD- alphaD- what does solute residues mean? Elvis Martis
- Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib David A Case
- [AMBER] Trouble installing amber tools on new OSX 10.13.1 Eiros Zamora, Juan
- Re: [AMBER] how to generate the force fied file of AsO3H3? David A Case
- [AMBER] Post processing of trajectory Sowmya Indrakumar
- Re: [AMBER] Post processing of trajectory Abdul-Rashid III Sampaco
- Re: [AMBER] Trouble installing amber tools on new OSX 10.13.1 Daniel Roe
- Re: [AMBER] Post processing of trajectory Sowmya Indrakumar
- Re: [AMBER] Trouble installing amber tools on new OSX 10.13.1 Hai Nguyen
- Re: [AMBER] how to generate the force fied file of AsO3H3? minyuan.mail.ustc.edu.cn
- Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib minyuan.mail.ustc.edu.cn
- [AMBER] imin=5 not working in AMBER16? Paul Mortenson
- Re: [AMBER] imin=5 not working in AMBER16? Cruzeiro,Vinicius Wilian D
- Re: [AMBER] imin=5 not working in AMBER16? Paul Mortenson
- Re: [AMBER] how to generate the force fied file of AsO3H3? Andrew Schaub
- Re: [AMBER] imin=5 not working in AMBER16? Cruzeiro,Vinicius Wilian D
- [AMBER] lipid 14 compatibility with FF14SB Chitrak Gupta
- [AMBER] Protein-Ligand Energy Minimization Kadir Tung
- Re: [AMBER] Trouble installing amber tools on new OSX 10.13.1 David A Case
- Re: [AMBER] lipid 14 compatibility with FF14SB Ross Walker
- Re: [AMBER] how to generate the force fied file of AsO3H3? MinYuan
- Re: [AMBER] how to generate the force fied file of AsO3H3? Pengfei Li
- Re: [AMBER] imin=5 not working in AMBER16? Paul Mortenson
Thursday, 30 November 2017
- [AMBER] MCPB.py how to insert the heteroatom heme in the one domain of macromolecule Rana Rehan Khalid
- [AMBER] antechamber: prepgen mainchain file character limit Markus Schneider
- Re: [AMBER] antechamber: prepgen mainchain file character limit Junmei Wang
- Re: [AMBER] lipid 14 compatibility with FF14SB Chitrak Gupta
- Re: [AMBER] antechamber: prepgen mainchain file character limit Markus Schneider
- Re: [AMBER] imin=5 not working in AMBER16? Daniel Roe
- Re: [AMBER] Protein-Ligand Energy Minimization Daniel Roe
- Re: [AMBER] Protein-Ligand Energy Minimization Carlos Simmerling
- [AMBER] PF6- octahedral geometry change during equilibration!! Sanaa ALAbbad
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! junmwang.gmail.com

Last message date: Thu Nov 30 2017 - 18:30:03 PST
Archived on: Fri Dec 20 2024 - 05:55:39 PST

Amber Archive Nov 2017 by date