Amber Archive May 2021 by thread
263 messages
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Starting
Fri Apr 30 2021 - 17:00:02 PDT,
Ending
Mon May 31 2021 - 21:00:02 PDT
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Re: [AMBER] installation of AmberTools 21
Qinghua Liao
(Fri Apr 30 2021 - 16:35:23 PDT)
Re: [AMBER] installation of AmberTools 21
David A Case
(Sat May 01 2021 - 05:20:23 PDT)
Re: [AMBER] installation of AmberTools 21
Rudy Richardson
(Sat May 01 2021 - 05:26:18 PDT)
Re: [AMBER] installation of AmberTools 21
David A Case
(Sat May 01 2021 - 05:40:48 PDT)
Re: [AMBER] installation of AmberTools 21
Rudy Richardson
(Sat May 01 2021 - 05:55:50 PDT)
Re: [AMBER] installation of AmberTools 21
Qinghua Liao
(Sun May 02 2021 - 06:45:59 PDT)
Re: [AMBER] Release of AmberTools21
Kshatresh Dutta Dubey
(Sat May 01 2021 - 04:40:23 PDT)
Re: [AMBER] [EXTERNAL] Release of AmberTools21
David A Case
(Sat May 01 2021 - 05:25:01 PDT)
Re: [AMBER] [EXTERNAL] Release of AmberTools21
Gustaf Olsson
(Thu May 06 2021 - 05:10:08 PDT)
Re: [AMBER] [EXTERNAL] Release of AmberTools21
David A Case
(Thu May 06 2021 - 05:34:47 PDT)
Re: [AMBER] [EXTERNAL] Release of AmberTools21
Gustaf Olsson
(Thu May 06 2021 - 05:51:29 PDT)
Re: [AMBER] [EXTERNAL] Release of AmberTools21
Gustaf Olsson
(Thu May 06 2021 - 05:59:00 PDT)
Re: [AMBER] [EXTERNAL] Release of AmberTools21
Gustaf Olsson
(Mon May 10 2021 - 03:54:50 PDT)
Re: [AMBER] [EXTERNAL] Release of AmberTools21
Gustaf Olsson
(Mon May 10 2021 - 04:09:27 PDT)
Re: [AMBER] [EXTERNAL] Release of AmberTools21
Gustaf Olsson
(Mon May 10 2021 - 06:00:47 PDT)
Re: [AMBER] [EXTERNAL] Release of AmberTools21
David A Case
(Mon May 10 2021 - 06:06:59 PDT)
Re: [AMBER] [EXTERNAL] Release of AmberTools21
Gustaf Olsson
(Mon May 10 2021 - 06:11:25 PDT)
Re: [AMBER] [EXTERNAL] Release of AmberTools21
Gustaf Olsson
(Mon May 10 2021 - 07:41:18 PDT)
Re: [AMBER] [EXTERNAL] Release of AmberTools21
Gerald Monard
(Tue May 11 2021 - 17:32:58 PDT)
Re: [AMBER] [EXTERNAL] Release of AmberTools21
Gustaf Olsson
(Mon May 10 2021 - 07:41:35 PDT)
Re: [AMBER] Installation Ambertools21 Mac M1 (arm64)
Florian Nachon
(Sat May 01 2021 - 05:49:43 PDT)
Re: [AMBER] Installation Ambertools21 Mac M1 (arm64)
David A Case
(Sat May 01 2021 - 09:51:00 PDT)
Re: [AMBER] Installation Ambertools21 Mac M1 (arm64)
Yoshitaka Moriwaki
(Sun May 02 2021 - 00:04:50 PDT)
Re: [AMBER] Installation Ambertools21 Mac M1 (arm64)
Florian Nachon
(Sun May 02 2021 - 04:38:41 PDT)
Re: [AMBER] Troubleshooting long idle times in pmemd.MPI
David A Case
(Sat May 01 2021 - 10:02:18 PDT)
Re: [AMBER] Troubleshooting long idle times in pmemd.MPI
Kevin Keane
(Sat May 01 2021 - 11:42:39 PDT)
Re: [AMBER] Troubleshooting long idle times in pmemd.MPI
David A Case
(Sun May 02 2021 - 05:30:29 PDT)
Re: [AMBER] polarizable FF in amber18 or 20
Ray Luo
(Sat May 01 2021 - 12:14:51 PDT)
Re: [AMBER] polarizable FF in amber18 or 20
Vaibhav Dixit
(Sat May 01 2021 - 23:35:25 PDT)
Re: [AMBER] polarizable FF in amber18 or 20
Ray Luo
(Mon May 03 2021 - 10:11:36 PDT)
Re: [AMBER] polarizable FF in amber18 or 20
Vaibhav Dixit
(Mon May 03 2021 - 11:02:43 PDT)
[AMBER] converting gromacs topology to amber
Ayesha Fatima
(Sun May 02 2021 - 09:32:31 PDT)
Re: [AMBER] converting gromacs topology to amber
Daniel Roe
(Mon May 03 2021 - 05:57:36 PDT)
Re: [AMBER] converting gromacs topology to amber
Ayesha Fatima
(Mon May 03 2021 - 06:30:12 PDT)
Re: [AMBER] converting gromacs topology to amber
Daniel Roe
(Mon May 03 2021 - 06:40:40 PDT)
Re: [AMBER] converting gromacs topology to amber
Ayesha Fatima
(Mon May 03 2021 - 06:49:23 PDT)
[AMBER] pmemd.cuda fails with "cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol"
Laura SCALVINI
(Mon May 03 2021 - 01:08:18 PDT)
Re: [AMBER] pmemd.cuda fails with "cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol"
David A Case
(Mon May 03 2021 - 05:11:08 PDT)
[AMBER] atom-order problem with prmtop and cpptraj
Vaibhav Dixit
(Mon May 03 2021 - 01:16:13 PDT)
Re: [AMBER] atom-order problem with prmtop and cpptraj
Vaibhav Dixit
(Mon May 03 2021 - 05:18:21 PDT)
Re: [AMBER] atom-order problem with prmtop and cpptraj
Daniel Roe
(Mon May 03 2021 - 05:47:16 PDT)
Re: [AMBER] atom-order problem with prmtop and cpptraj
David A Case
(Mon May 03 2021 - 05:26:05 PDT)
Re: [AMBER] atom-order problem with prmtop and cpptraj
Vaibhav Dixit
(Mon May 03 2021 - 05:39:09 PDT)
[AMBER] Error due to faulty Connection atoms
Guillem Vila I Julià
(Mon May 03 2021 - 03:11:25 PDT)
Re: [AMBER] Error due to faulty Connection atoms
David A Case
(Wed May 12 2021 - 06:11:24 PDT)
Re: [AMBER] Error due to faulty Connection atoms
Guillem Vila I Julià
(Wed May 19 2021 - 06:25:15 PDT)
[AMBER] Distance between nucleotides and amino acids
Airy Sanjeev
(Mon May 03 2021 - 03:19:47 PDT)
Re: [AMBER] Distance between nucleotides and amino acids
Daniel Roe
(Mon May 03 2021 - 06:11:58 PDT)
[AMBER] CPPTRAJ nativecontacts
Richard Kullmann
(Mon May 03 2021 - 07:28:36 PDT)
Re: [AMBER] CPPTRAJ nativecontacts
Daniel Roe
(Mon May 03 2021 - 08:48:13 PDT)
Re: [AMBER] CPPTRAJ nativecontacts
Richard Kullmann
(Mon May 10 2021 - 06:29:46 PDT)
Re: [AMBER] CPPTRAJ nativecontacts
Daniel Roe
(Tue May 11 2021 - 12:21:44 PDT)
[AMBER] MMPBSA calculation error
Yogeshwaran Krishnan
(Tue May 04 2021 - 05:09:25 PDT)
Re: [AMBER] trpcage benchmark: reduce 32x or dimerize ?
Scott Brozell
(Tue May 04 2021 - 12:37:05 PDT)
[AMBER] converting gromacs topology to amber
Ayesha Fatima
(Tue May 04 2021 - 15:04:26 PDT)
Re: [AMBER] converting gromacs topology to amber
David A Case
(Wed May 05 2021 - 05:04:37 PDT)
[AMBER] N6-myristoyl lysine parameters
Mark Fisher
(Tue May 04 2021 - 19:02:39 PDT)
[AMBER] Query about AmberTools21 conda distribution
Jan Brezovsky
(Wed May 05 2021 - 00:52:31 PDT)
Re: [AMBER] Query about AmberTools21 conda distribution
David A Case
(Sun May 09 2021 - 12:59:44 PDT)
[AMBER] guidance for microsecond long MD simulations
Vaibhav Dixit
(Wed May 05 2021 - 10:10:24 PDT)
Re: [AMBER] guidance for microsecond long MD simulations
David A Case
(Wed May 05 2021 - 11:42:59 PDT)
[AMBER] Inconsistent results on TI with cpu vs gpu code
Giorgos Lambrinidis
(Wed May 05 2021 - 10:42:58 PDT)
[AMBER] Questions about QM/MM simulations
马芳芳
(Wed May 05 2021 - 18:55:39 PDT)
Re: [AMBER] Questions about QM/MM simulations
Goetz, Andreas
(Wed May 05 2021 - 21:40:35 PDT)
[AMBER] AMBER20/AMBERTools21 Installation Errors when compiling mpich
石谷沁
(Thu May 06 2021 - 00:56:19 PDT)
Re: [AMBER] AMBER20/AMBERTools21 Installation Errors when compiling mpich
David A Case
(Thu May 06 2021 - 05:14:09 PDT)
[AMBER] 答复: [ambermd.org代发]Re: AMBER20/AMBERTools21 Installation Errors when compiling mpich
石谷沁
(Thu May 06 2021 - 17:49:21 PDT)
Re: [AMBER] 答复: [ambermd.org代发]Re: AMBER20/AMBERTools21 Installation Errors when compiling mpich
David A Case
(Fri May 07 2021 - 05:14:07 PDT)
Re: [AMBER] [ambermd.org代发]Re: AMBER20/AMBERTools21 Installation Errors when compiling mpich
石谷沁
(Thu May 06 2021 - 06:40:12 PDT)
Re: [AMBER] [ambermd.org代发]Re: AMBER20/AMBERTools21 Installation Errors when compiling mpich
石谷沁
(Fri May 07 2021 - 01:53:34 PDT)
[AMBER] Difficulty in doing umbrella sampling using LCOD method
Soumyajit Karmakar
(Thu May 06 2021 - 08:21:19 PDT)
[AMBER] differences in counterion position with water models and questions
Vaibhav Dixit
(Thu May 06 2021 - 23:07:13 PDT)
Re: [AMBER] differences in counterion position with water models and questions
Dr. Anselm Horn
(Mon May 10 2021 - 05:37:52 PDT)
Re: [AMBER] differences in counterion position with water models and questions
Vaibhav Dixit
(Wed May 12 2021 - 09:20:40 PDT)
[AMBER] understanding DSSP outout
Sadaf Rani
(Thu May 06 2021 - 23:53:06 PDT)
Re: [AMBER] understanding DSSP outout
Daniel Roe
(Fri May 14 2021 - 08:42:05 PDT)
Re: [AMBER] Questions about QM/MM simulations (Goetz, Andreas)
马芳芳
(Fri May 07 2021 - 01:48:21 PDT)
Re: [AMBER] Questions about QM/MM simulations (Goetz, Andreas)
Goetz, Andreas
(Fri May 07 2021 - 12:05:34 PDT)
[AMBER] Amber20 CUDA.serial tests comparison failed with gb calculation: differences at e-01 level
石谷沁
(Fri May 07 2021 - 02:19:24 PDT)
Re: [AMBER] Amber20 CUDA.serial tests comparison failed with gb calculation: differences at e-01 level
David A Case
(Fri May 07 2021 - 05:30:56 PDT)
[AMBER] 答复: [ambermd.org代发]Re: Amber20 CUDA.serial tests comparison failed with gb calculation: differences at e-01 level
石谷沁
(Fri May 07 2021 - 20:03:25 PDT)
[AMBER] Avoiding steric snafus with protein mutations in tleap?
Tucker Burgin
(Fri May 07 2021 - 08:36:52 PDT)
Re: [AMBER] Avoiding steric snafus with protein mutations in tleap?
Matias Machado
(Sat May 08 2021 - 11:15:29 PDT)
[AMBER] Digest of issues installing AMBER21 in Centos 7
Azurmendi, Hugo
(Sat May 08 2021 - 10:00:26 PDT)
Re: [AMBER] Digest of issues installing AMBER21 in Centos 7
David A Case
(Sun May 09 2021 - 05:46:51 PDT)
[AMBER] Query regarding density analysis
ARITRA MITRA
(Sun May 09 2021 - 08:12:40 PDT)
[AMBER] Inconsistent results on TI with cpu vs gpu code
Giorgos Lambrinidis
(Sun May 09 2021 - 09:19:12 PDT)
Re: [AMBER] Inconsistent results on TI with cpu vs gpu code
David A Case
(Sun May 09 2021 - 12:56:04 PDT)
[AMBER] MBAR energies when using soft-core potential in pmemd TI
Hosein Geraili Daronkola
(Sun May 09 2021 - 15:15:01 PDT)
Re: [AMBER] MBAR energies when using soft-core potential in pmemd TI
David A Case
(Mon May 10 2021 - 06:00:31 PDT)
Re: [AMBER] MBAR energies when using soft-core potential in pmemd TI
Brian Radak
(Mon May 10 2021 - 06:21:56 PDT)
[AMBER] Test
Goetz, Andreas
(Sun May 09 2021 - 18:03:14 PDT)
[AMBER] stacking interactions represented by force field equation?
Martin Rosellen
(Mon May 10 2021 - 07:31:31 PDT)
Re: [AMBER] stacking interactions represented by force field equation?
Carlos Simmerling
(Mon May 10 2021 - 07:52:55 PDT)
Re: [AMBER] stacking interactions represented by force field equation?
Jiri Sponer
(Mon May 10 2021 - 09:02:38 PDT)
Re: [AMBER] stacking interactions represented by force field equation?
Matias Machado
(Tue May 11 2021 - 08:40:20 PDT)
Re: [AMBER] stacking interactions represented by force field equation?
Jiri Sponer
(Tue May 11 2021 - 10:04:20 PDT)
[AMBER] Keeping input protein hydrogens?
Markus Metz
(Mon May 10 2021 - 09:48:36 PDT)
Re: [AMBER] Keeping input protein hydrogens?
David A Case
(Mon May 10 2021 - 13:58:28 PDT)
[AMBER] FEW MMGBSA calculation
Yogeshwaran Krishnan
(Tue May 11 2021 - 02:10:15 PDT)
[AMBER] solvent accessibility
Cato, Lee
(Tue May 11 2021 - 09:20:13 PDT)
Re: [AMBER] solvent accessibility
Daniel Roe
(Fri May 14 2021 - 11:04:20 PDT)
Re: [AMBER] solvent accessibility
David A Case
(Fri May 14 2021 - 18:22:04 PDT)
Re: [AMBER] solvent accessibility
German P. Barletta
(Sat May 15 2021 - 12:41:01 PDT)
Re: [AMBER] solvent accessibility
David A Case
(Sat May 15 2021 - 13:00:33 PDT)
[AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again.
ARITRA MITRA
(Tue May 11 2021 - 11:02:38 PDT)
Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again.
Daniel Roe
(Tue May 11 2021 - 12:09:03 PDT)
Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again.
ARITRA MITRA
(Thu May 13 2021 - 07:34:06 PDT)
Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again.
Daniel Roe
(Thu May 13 2021 - 08:02:05 PDT)
Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again.
ARITRA MITRA
(Thu May 13 2021 - 08:06:14 PDT)
Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again.
Daniel Roe
(Thu May 13 2021 - 09:26:02 PDT)
[AMBER] Error Installing Amber20 on group's cluster
Min Chiang Gary Ong
(Tue May 11 2021 - 19:58:04 PDT)
Re: [AMBER] Error Installing Amber20 on group's cluster
David A Case
(Wed May 12 2021 - 05:50:35 PDT)
Re: [AMBER] Error Installing Amber20 on group's cluster
Min Chiang Gary Ong
(Wed May 12 2021 - 08:11:17 PDT)
[AMBER] AMBER 18 citation endnote file
Athena N
(Tue May 11 2021 - 23:16:36 PDT)
[AMBER] MMPBSA.py and rms fit: Results depend on reference frame
Lennart Gundelach
(Wed May 12 2021 - 00:33:55 PDT)
Re: [AMBER] MMPBSA.py and rms fit: Results depend on reference frame
David A Case
(Wed May 12 2021 - 06:00:55 PDT)
Re: [AMBER] MMPBSA.py and rms fit: Results depend on reference frame
Lennart Gundelach
(Thu May 27 2021 - 02:07:15 PDT)
[AMBER] Amber stuck on Control data for the run
Victoria E Hill
(Wed May 12 2021 - 03:11:49 PDT)
Re: [AMBER] Amber stuck on Control data for the run
David A Case
(Wed May 12 2021 - 06:07:01 PDT)
Re: [AMBER] Amber stuck on Control data for the run
Daniel Roe
(Wed May 12 2021 - 06:47:37 PDT)
Re: [AMBER] Amber stuck on Control data for the run
Matias Machado
(Wed May 12 2021 - 07:00:41 PDT)
[AMBER] Effect of noisy force calculations
Thomas Fox
(Wed May 12 2021 - 06:49:48 PDT)
[AMBER] Mutate double stranded DNA?
Gustavo Seabra
(Wed May 12 2021 - 18:01:42 PDT)
Re: [AMBER] Mutate double stranded DNA?
Mariano Curti
(Thu May 13 2021 - 00:29:18 PDT)
Re: [AMBER] Mutate double stranded DNA?
Carlos Simmerling
(Thu May 13 2021 - 01:59:19 PDT)
Re: [AMBER] Mutate double stranded DNA?
Vlad Cojocaru
(Thu May 13 2021 - 03:45:46 PDT)
Re: [AMBER] Mutate double stranded DNA?
Gustavo Seabra
(Thu May 13 2021 - 11:25:00 PDT)
Re: [AMBER] Mutate double stranded DNA?
Vlad Cojocaru
(Fri May 14 2021 - 09:03:41 PDT)
[AMBER] AmberTools21 cmake build
H. Kawasaki
(Wed May 12 2021 - 23:49:40 PDT)
Re: [AMBER] AmberTools21 cmake build
David A Case
(Thu May 13 2021 - 05:56:02 PDT)
[AMBER] How to calculate the contribution to protein-protein aggregation from hydrophobic interactions ?
刘为
(Thu May 13 2021 - 06:05:05 PDT)
[AMBER] Selenomethionine force field parameters
Rafał Madaj
(Thu May 13 2021 - 10:50:25 PDT)
Re: [AMBER] Selenomethionine force field parameters
Kellon Belfon
(Thu May 13 2021 - 17:14:55 PDT)
Re: [AMBER] Selenomethionine force field parameters
David A Case
(Thu May 13 2021 - 18:45:09 PDT)
Re: [AMBER] Selenomethionine force field parameters
Kellon Belfon
(Thu May 13 2021 - 20:35:25 PDT)
Re: [AMBER] Selenomethionine force field parameters
Jeffrey Wagner
(Fri May 14 2021 - 07:54:44 PDT)
Re: [AMBER] Selenomethionine force field parameters
David A Case
(Fri May 14 2021 - 09:01:17 PDT)
Re: [AMBER] Selenomethionine force field parameters
Jeffrey Wagner
(Fri May 14 2021 - 10:57:18 PDT)
Re: [AMBER] Selenomethionine force field parameters
Kellon Belfon
(Fri May 14 2021 - 11:57:44 PDT)
Re: [AMBER] Selenomethionine force field parameters
Jeffrey Wagner
(Fri May 14 2021 - 14:05:36 PDT)
Re: [AMBER] Selenomethionine force field parameters
Rafał Madaj
(Fri May 14 2021 - 23:58:26 PDT)
Re: [AMBER] Selenomethionine force field parameters
Kellon Belfon
(Sat May 15 2021 - 07:46:26 PDT)
Re: [AMBER] Selenomethionine force field parameters
Kellon Belfon
(Sat May 15 2021 - 14:23:31 PDT)
Re: [AMBER] Selenomethionine force field parameters
Rafał Madaj
(Sat May 15 2021 - 15:05:54 PDT)
Re: [AMBER] Selenomethionine force field parameters
Kellon Belfon
(Sat May 15 2021 - 15:26:18 PDT)
[AMBER] New In CPPTRAJ (May 2021)
Daniel Roe
(Thu May 13 2021 - 11:50:29 PDT)
Re: [AMBER] New In CPPTRAJ (May 2021)
xichen li
(Fri May 14 2021 - 02:37:30 PDT)
Re: [AMBER] New In CPPTRAJ (May 2021)
Daniel Roe
(Fri May 14 2021 - 11:00:01 PDT)
[AMBER] Error running make install
Rodrigo da Silva Bitzer
(Thu May 13 2021 - 13:33:29 PDT)
Re: [AMBER] Error running make install
David A Case
(Fri May 14 2021 - 05:33:57 PDT)
Re: [AMBER] Error running make install
Rodrigo da Silva Bitzer
(Fri May 14 2021 - 14:24:37 PDT)
[AMBER] CPPTRAJ nastruct not recognising G-U wobble base pairs
Francis Acquah
(Thu May 13 2021 - 15:48:36 PDT)
Re: [AMBER] CPPTRAJ nastruct not recognising G-U wobble base pairs
Daniel Roe
(Fri May 14 2021 - 11:02:07 PDT)
[AMBER] Cpptraj segfaults on single REMD trajectories?
Brian Radak
(Fri May 14 2021 - 08:19:29 PDT)
Re: [AMBER] Cpptraj segfaults on single REMD trajectories?
Daniel Roe
(Fri May 14 2021 - 08:32:20 PDT)
Re: [AMBER] Cpptraj segfaults on single REMD trajectories?
Brian Radak
(Fri May 14 2021 - 10:40:40 PDT)
Re: [AMBER] Cpptraj segfaults on single REMD trajectories?
Daniel Roe
(Fri May 14 2021 - 10:57:27 PDT)
[AMBER] Problem re. non-integer charge in glycoprotein
RAJAS MALLENAHALLI RAO
(Fri May 14 2021 - 09:24:07 PDT)
Re: [AMBER] Problem re. non-integer charge in glycoprotein
Dr. Anselm Horn
(Mon May 17 2021 - 03:42:04 PDT)
Re: [AMBER] Problem re. non-integer charge in glycoprotein
RAJAS MALLENAHALLI RAO
(Mon May 17 2021 - 05:23:36 PDT)
[AMBER] Multiple Dihedral Parameters
Abdul Basit
(Sun May 16 2021 - 09:51:03 PDT)
Re: [AMBER] Multiple Dihedral Parameters
David A Case
(Sun May 16 2021 - 12:09:44 PDT)
[AMBER] MMGBSA using charmm36 force field-- positive value
周丽萍
(Sun May 16 2021 - 18:21:39 PDT)
[AMBER] Surprisingly Poor Performance of Quadro RTX5000 -- Any Ideas on Reasons...
石谷沁
(Sun May 16 2021 - 18:53:56 PDT)
[AMBER] Miniconda pkg install error
H. Kawasaki
(Mon May 17 2021 - 00:35:07 PDT)
Re: [AMBER] Miniconda pkg install error
David A Case
(Mon May 17 2021 - 05:30:02 PDT)
[AMBER] Algorithm Details of Addions/Addions2
Robert Molt
(Mon May 17 2021 - 09:12:37 PDT)
Re: [AMBER] Algorithm Details of Addions/Addions2
David A Case
(Thu May 20 2021 - 06:15:17 PDT)
[AMBER] CMake Error at cmake/jedbrown/FindFFTW.cmake:307 (add_library):
Akinyemi Omoniyi
(Tue May 18 2021 - 02:03:26 PDT)
Re: [AMBER] CMake Error at cmake/jedbrown/FindFFTW.cmake:307 (add_library):
David A Case
(Tue May 18 2021 - 05:32:22 PDT)
Re: [AMBER] CMake Error at cmake/jedbrown/FindFFTW.cmake:307 (add_library):
Akinyemi Omoniyi
(Wed May 19 2021 - 21:46:31 PDT)
[AMBER] Combining GLYCAM and AMBER/GAFF
Gustaf Olsson
(Tue May 18 2021 - 06:25:30 PDT)
Re: [AMBER] Combining GLYCAM and AMBER/GAFF
David A Case
(Thu May 20 2021 - 06:10:42 PDT)
Re: [AMBER] Combining GLYCAM and AMBER/GAFF
Lachele Foley
(Thu May 20 2021 - 19:32:21 PDT)
Re: [AMBER] Combining GLYCAM and AMBER/GAFF
Gustaf Olsson
(Thu May 20 2021 - 23:49:46 PDT)
[AMBER] Applying change to van der Waals for specific pairs of atom
Smith, Richard
(Tue May 18 2021 - 13:43:51 PDT)
Re: [AMBER] Applying change to van der Waals for specific pairs of atom
Song, Lin
(Wed May 19 2021 - 15:03:55 PDT)
Re: [AMBER] Applying change to van der Waals for specific pairs of atom
David A Case
(Thu May 20 2021 - 06:08:06 PDT)
[AMBER] Conformation search speed increase with Cartesian restraints
Liao
(Tue May 18 2021 - 20:41:58 PDT)
Re: [AMBER] Conformation search speed increase with Cartesian restraints
Charo del Genio
(Wed May 19 2021 - 10:25:51 PDT)
Re: [AMBER] Conformation search speed increase with Cartesian restraints
Liao
(Wed May 19 2021 - 14:02:32 PDT)
Re: [AMBER] Conformation search speed increase with Cartesian restraints
Charo del Genio
(Thu May 20 2021 - 04:40:15 PDT)
[AMBER] Lite Hash Rate and pmemd.cuda
Alessandro Contini
(Wed May 19 2021 - 01:12:05 PDT)
[AMBER] How do I generate prmtop file for system containing more than 1 ligand?
Min Chiang Gary Ong
(Wed May 19 2021 - 06:24:13 PDT)
Re: [AMBER] How do I generate prmtop file for system containing more than 1 ligand?
Carlos Simmerling
(Wed May 19 2021 - 09:19:40 PDT)
Re: [AMBER] How do I generate prmtop file for system containing more than 1 ligand?
David A Case
(Wed May 19 2021 - 10:22:23 PDT)
[AMBER] Compiling Fortran on M1 chipset
Joe Leonard
(Wed May 19 2021 - 10:11:36 PDT)
[AMBER] Restraints and TI in absolute binding free energies
Hans De Winter
(Thu May 20 2021 - 03:39:25 PDT)
Re: [AMBER] AMBER/EVB
David A Case
(Thu May 20 2021 - 06:25:08 PDT)
[AMBER] Covalent bonds across periodic boundaries supported yet/ever?
Tucker Burgin
(Thu May 20 2021 - 08:58:59 PDT)
Re: [AMBER] Covalent bonds across periodic boundaries supported yet/ever?
David A Case
(Wed May 26 2021 - 06:08:31 PDT)
Re: [AMBER] Covalent bonds across periodic boundaries supported yet/ever?
Matias Machado
(Wed May 26 2021 - 13:14:38 PDT)
Re: [AMBER] Covalent bonds across periodic boundaries supported yet/ever?
Thomas Cheatham
(Wed May 26 2021 - 13:27:16 PDT)
[AMBER] AMberTools21 installation
Neha Gandhi
(Fri May 21 2021 - 23:40:34 PDT)
Re: [AMBER] AMberTools21 installation
Gustaf Olsson
(Sun May 23 2021 - 23:33:58 PDT)
Re: [AMBER] AMberTools21 installation
Neha Gandhi
(Mon May 24 2021 - 02:39:55 PDT)
Re: [AMBER] AMberTools21 installation
Gustaf Olsson
(Mon May 24 2021 - 02:59:53 PDT)
Re: [AMBER] AMberTools21 installation
David A Case
(Wed May 26 2021 - 06:12:46 PDT)
[AMBER] Query about AmberTools21 conda distribution
David A Case
(Sat May 22 2021 - 05:08:08 PDT)
Re: [AMBER] Query about AmberTools21 conda distribution
Jan Brezovsky
(Sat May 22 2021 - 08:09:21 PDT)
[AMBER] Clustering getting killed
Sruthi Sudhakar
(Sat May 22 2021 - 06:43:09 PDT)
Re: [AMBER] Clustering getting killed
Carlos Simmerling
(Sat May 22 2021 - 08:18:49 PDT)
Re: [AMBER] Clustering getting killed
Daniel Roe
(Sat May 22 2021 - 10:28:07 PDT)
Re: [AMBER] Clustering getting killed
Daniel Roe
(Sat May 22 2021 - 10:29:10 PDT)
[AMBER] distance matrix all atoms
Fabian Glaser
(Mon May 24 2021 - 06:59:58 PDT)
Re: [AMBER] distance matrix all atoms
Daniel Roe
(Mon May 24 2021 - 08:36:02 PDT)
[AMBER] Residue-Ligand binding free energy calculations
Rana Rehan Khalid
(Mon May 24 2021 - 10:16:05 PDT)
Re: [AMBER] Residue-Ligand binding free energy calculations
Carlos Simmerling
(Mon May 24 2021 - 10:20:36 PDT)
Re: [AMBER] Residue-Ligand binding free energy calculations
Rana Rehan Khalid
(Mon May 24 2021 - 10:26:13 PDT)
[AMBER] - Including ion type of interactions in free energy calculation
Patil Pranita Uttamrao
(Mon May 24 2021 - 22:34:20 PDT)
Re: [AMBER] - Including ion type of interactions in free energy calculation
David A Case
(Wed May 26 2021 - 07:27:44 PDT)
[AMBER] - DFT method for heme QM calculation
Patil Pranita Uttamrao
(Tue May 25 2021 - 01:46:13 PDT)
Re: [AMBER] - DFT method for heme QM calculation
Dawid das
(Tue May 25 2021 - 06:30:25 PDT)
[AMBER] Joining two molecules
Gustaf Olsson
(Tue May 25 2021 - 03:19:30 PDT)
Re: [AMBER] Joining two molecules
Daniel Roe
(Tue May 25 2021 - 06:38:51 PDT)
Re: [AMBER] Joining two molecules
Gustaf Olsson
(Wed May 26 2021 - 00:48:40 PDT)
Re: [AMBER] Joining two molecules
Gustaf Olsson
(Wed May 26 2021 - 02:16:47 PDT)
Re: [AMBER] Joining two molecules
Gustaf Olsson
(Wed May 26 2021 - 05:44:56 PDT)
Re: [AMBER] Joining two molecules
Daniel Roe
(Wed May 26 2021 - 06:33:26 PDT)
Re: [AMBER] Joining two molecules
Gustaf Olsson
(Fri May 28 2021 - 01:44:19 PDT)
Re: [AMBER] Joining two molecules
Daniel Roe
(Fri May 28 2021 - 02:34:35 PDT)
Re: [AMBER] Joining two molecules
Gustaf Olsson
(Fri May 28 2021 - 02:47:27 PDT)
Re: [AMBER] Joining two molecules
Daniel Roe
(Fri May 28 2021 - 06:25:09 PDT)
Re: [AMBER] Joining two molecules
Gustaf Olsson
(Mon May 31 2021 - 00:37:12 PDT)
Re: [AMBER] Joining two molecules
Gustaf Olsson
(Mon May 31 2021 - 02:34:18 PDT)
Re: [AMBER] Joining two molecules
Dr. Anselm Horn
(Tue May 25 2021 - 07:05:45 PDT)
Re: [AMBER] Joining two molecules
Gustaf Olsson
(Wed May 26 2021 - 00:49:31 PDT)
Re: [AMBER] Joining two molecules
Gustaf Olsson
(Wed May 26 2021 - 00:51:26 PDT)
[AMBER] kindly help with this mmpbsa.py.MPI error
Gargi Bhattacharya
(Tue May 25 2021 - 03:44:01 PDT)
Re: [AMBER] kindly help with this mmpbsa.py.MPI error
Daniel Roe
(Tue May 25 2021 - 06:40:02 PDT)
[AMBER] test message
David A Case
(Tue May 25 2021 - 05:13:54 PDT)
Re: [AMBER] DFT method for heme QM calculationPranita,
Matthew Guberman-Pfeffer
(Tue May 25 2021 - 12:26:21 PDT)
Re: [AMBER] DFT method for heme QM calculationPranita,
Robert Molt
(Tue May 25 2021 - 12:51:46 PDT)
[AMBER] Umbrella sampling
Rana Rehan Khalid
(Tue May 25 2021 - 15:00:35 PDT)
Re: [AMBER] Umbrella sampling
David A Case
(Wed May 26 2021 - 06:26:59 PDT)
Re: [AMBER] Umbrella sampling
Thomas Cheatham
(Wed May 26 2021 - 10:28:24 PDT)
[AMBER] ligand receptor dissociation study
Rana Rehan Khalid
(Wed May 26 2021 - 09:23:04 PDT)
Re: [AMBER] ligand receptor dissociation study
Song, Lin
(Wed May 26 2021 - 09:39:04 PDT)
[AMBER] Umbrella Sampling error
Rana Rehan Khalid
(Wed May 26 2021 - 14:56:12 PDT)
[AMBER] Seek a solution for can't generate the mol2 files for the metal site residues
Huimin Tian
(Wed May 26 2021 - 18:33:33 PDT)
Re: [AMBER] Seek a solution for can't generate the mol2 files for the metal site residues
Daniel Roe
(Thu May 27 2021 - 06:30:29 PDT)
[AMBER] MMGB/PBSA ligand with lone pair
Katia Galentino
(Thu May 27 2021 - 01:55:37 PDT)
Re: [AMBER] MMGB/PBSA ligand with lone pair
David A Case
(Thu May 27 2021 - 07:12:34 PDT)
Re: [AMBER] xleap
David A Case
(Thu May 27 2021 - 05:08:45 PDT)
[AMBER] A bug in PMEMD which may cause aray (ti_dvdl_values) index out-of-boundary error
Ye Mei
(Thu May 27 2021 - 17:54:46 PDT)
[AMBER] Fortran runtime error:
Ephraim Marondedze
(Fri May 28 2021 - 01:13:48 PDT)
Re: [AMBER] Fortran runtime error:
David A Case
(Fri May 28 2021 - 07:12:04 PDT)
Re: [AMBER] Fortran runtime error:
Ephraim Marondedze
(Fri May 28 2021 - 23:09:03 PDT)
[AMBER] Simulating dehydrated bilayers with a vacuum above and below
Blake Armstrong
(Fri May 28 2021 - 01:37:39 PDT)
[AMBER] Regarding the forcefield parameters for cytochrome P450 heme group
Patil Pranita Uttamrao
(Fri May 28 2021 - 12:39:00 PDT)
Re: [AMBER] Regarding the forcefield parameters for cytochrome P450 heme group
Vaibhav Dixit
(Fri May 28 2021 - 22:21:01 PDT)
Re: [AMBER] MULTI_RMSD NFE-Error : Cannot read &colvar namelist!
Feng Pan
(Fri May 28 2021 - 22:07:57 PDT)
Re: [AMBER] MULTI_RMSD NFE-Error : Cannot read &colvar namelist!
Luis Simon
(Sat May 29 2021 - 05:35:39 PDT)
Re: [AMBER] MULTI_RMSD NFE-Error : Cannot read &colvar namelist!
Feng Pan
(Sat May 29 2021 - 11:49:09 PDT)
[AMBER] Umbrella sampling (Protein Receptor--ligand)
Rana Rehan Khalid
(Sat May 29 2021 - 14:44:39 PDT)
Re: [AMBER] Umbrella sampling (Protein Receptor--ligand)
David A Case
(Sun May 30 2021 - 17:31:59 PDT)
[AMBER] Error: Could not open file frcmod.ions1lm_126_hfe_opc: not found
Akinyemi Omoniyi
(Sat May 29 2021 - 21:39:39 PDT)
Re: [AMBER] Error: Could not open file frcmod.ions1lm_126_hfe_opc: not found
David A Case
(Sun May 30 2021 - 05:05:08 PDT)
Re: [AMBER] Error: Could not open file frcmod.ions1lm_126_hfe_opc: not found
Akinyemi Omoniyi
(Sun May 30 2021 - 05:48:57 PDT)
[AMBER] APR- Umbrella sampling of Receptor- ligand complex
Rana Rehan Khalid
(Sun May 30 2021 - 12:38:54 PDT)
Re: [AMBER] APR- Umbrella sampling of Receptor- ligand complex
Niel Henriksen
(Mon May 31 2021 - 20:37:49 PDT)
[AMBER] Error in pca analysis
Sruthi Sudhakar
(Mon May 31 2021 - 10:21:31 PDT)
Last message date
:
Mon May 31 2021 - 21:00:02 PDT
Archived on
: Fri Nov 15 2024 - 05:56:10 PST
263 messages
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