Amber Archive Nov 2020 by thread
285 messages
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Starting
Sat Oct 31 2020 - 23:30:02 PDT,
Ending
Mon Nov 30 2020 - 10:30:02 PST
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Re: [AMBER] how find Es from mdout to estimate vertical energy gap
Vaibhav Dixit
(Sat Oct 31 2020 - 23:05:54 PDT)
[AMBER] Aqvist force field for magnesium
Jenny 148
(Sun Nov 01 2020 - 00:09:52 PDT)
Re: [AMBER] Aqvist force field for magnesium
Pengfei Li
(Fri Nov 20 2020 - 08:32:28 PST)
Re: [AMBER] NMR restraints
Debarati DasGupta
(Sun Nov 01 2020 - 06:19:14 PST)
Re: [AMBER] NMR restraints
David A Case
(Mon Nov 02 2020 - 04:19:40 PST)
Re: [AMBER] NMR restraints
Debarati DasGupta
(Mon Nov 02 2020 - 14:19:50 PST)
Re: [AMBER] NMR restraints
Debarati DasGupta
(Mon Nov 02 2020 - 14:21:27 PST)
[AMBER] RESTARTED DUE TO LINMIN FAILURE ...
Sadaf Rani
(Sun Nov 01 2020 - 07:21:01 PST)
Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE ...
David A Case
(Mon Nov 02 2020 - 04:22:52 PST)
Re: [AMBER] Tri-coordination environment in zinc
SATYAJIT KHATUA
(Sun Nov 01 2020 - 09:38:42 PST)
Re: [AMBER] Tri-coordination environment in zinc
Bill Ross
(Sun Nov 01 2020 - 10:35:31 PST)
Re: [AMBER] Tri-coordination environment in zinc
SATYAJIT KHATUA
(Mon Nov 02 2020 - 21:06:14 PST)
Re: [AMBER] Tri-coordination environment in zinc
Pengfei Li
(Fri Nov 20 2020 - 07:42:47 PST)
Re: [AMBER] Tri-coordination environment in zinc
SATYAJIT KHATUA
(Sat Nov 21 2020 - 02:01:29 PST)
Re: [AMBER] MMGBSA/MMPBSA Help
Abdul-Rashid III Sampaco
(Sun Nov 01 2020 - 21:07:56 PST)
[AMBER] Screenshots for publications
Gustaf Olsson
(Mon Nov 02 2020 - 02:05:28 PST)
Re: [AMBER] Screenshots for publications
David A Case
(Mon Nov 02 2020 - 04:23:34 PST)
[AMBER] Understanding restraint files generated from CHARMM-GUI
Souvik Dey
(Mon Nov 02 2020 - 11:05:45 PST)
Re: [AMBER] Understanding restraint files generated from CHARMM-GUI
David A Case
(Mon Nov 02 2020 - 13:19:20 PST)
[AMBER] MM/PBSA after minimization
h_sahakyan.mb.sci.am
(Mon Nov 02 2020 - 11:12:00 PST)
Re: [AMBER] MM/PBSA after minimization
Elvis Martis
(Mon Nov 02 2020 - 17:35:08 PST)
[AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference
Sarah Jane
(Mon Nov 02 2020 - 16:39:05 PST)
Re: [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference
David A Case
(Mon Nov 02 2020 - 17:58:54 PST)
[AMBER] Protein-nucleic acid interactions
Athena N
(Mon Nov 02 2020 - 21:20:10 PST)
Re: [AMBER] Protein-nucleic acid interactions
Bill Ross
(Mon Nov 02 2020 - 22:23:00 PST)
Re: [AMBER] System preparation for MMPBSA.py
SATYAJIT KHATUA
(Mon Nov 02 2020 - 21:53:40 PST)
Re: [AMBER] System preparation for MMPBSA.py
David A Case
(Tue Nov 03 2020 - 05:57:32 PST)
Re: [AMBER] System preparation for MMPBSA.py
SATYAJIT KHATUA
(Tue Nov 03 2020 - 21:49:38 PST)
Re: [AMBER] System preparation for MMPBSA.py
David A Case
(Wed Nov 04 2020 - 05:09:15 PST)
Re: [AMBER] System preparation for MMPBSA.py
SATYAJIT KHATUA
(Wed Nov 04 2020 - 23:08:48 PST)
Re: [AMBER] System preparation for MMPBSA.py
David A Case
(Thu Nov 05 2020 - 05:37:10 PST)
Re: [AMBER] System preparation for MMPBSA.py
Pengfei Li
(Fri Nov 20 2020 - 08:02:16 PST)
[AMBER] Error while running MMGBSA
Suchetana Gupta
(Mon Nov 02 2020 - 22:26:07 PST)
Re: [AMBER] Error while running MMGBSA
David A Case
(Tue Nov 03 2020 - 06:01:37 PST)
[AMBER] installation issues with cuda 11.1
Demian Riccardi
(Tue Nov 03 2020 - 10:16:57 PST)
[AMBER] PCA with multiple peaks
Abhilash J
(Tue Nov 03 2020 - 13:34:42 PST)
Re: [AMBER] Help with parameterization of non-standard amino acid
Amit Sharma (Asstt. Prof., MCARS)
(Wed Nov 04 2020 - 01:30:31 PST)
Re: [AMBER] Help with parameterization of non-standard amino acid
David A Case
(Wed Nov 04 2020 - 05:15:40 PST)
Re: [AMBER] Help with parameterization of non-standard amino acid
Amit Sharma (Asstt. Prof., MCARS)
(Wed Nov 04 2020 - 08:22:54 PST)
Re: [AMBER] Help with parameterization of non-standard amino acid
Carlos Simmerling
(Wed Nov 04 2020 - 08:58:12 PST)
Re: [AMBER] Help with parameterization of non-standard amino acid
Dr. Anselm Horn
(Thu Nov 05 2020 - 03:50:06 PST)
Re: [AMBER] Help with parameterization of non-standard amino acid
Carlos Simmerling
(Thu Nov 05 2020 - 10:04:43 PST)
Re: [AMBER] Help with parameterization of non-standard amino acid
Dr. Anselm Horn
(Fri Nov 06 2020 - 02:15:24 PST)
Re: [AMBER] Help with parameterization of non-standard amino acid
Pengfei Li
(Fri Nov 20 2020 - 08:24:41 PST)
[AMBER] Question about the outfile of 'softcore part'
wangjianing_mail
(Wed Nov 04 2020 - 03:08:36 PST)
[AMBER] Question about the 'softcore part' of outputfile in pmemd
wangjianing_mail
(Wed Nov 04 2020 - 03:09:37 PST)
[AMBER] Saving pdb as parm7/prmtop file with boundary conditions
Aashish Shivkumar
(Thu Nov 05 2020 - 00:11:04 PST)
Re: [AMBER] Saving pdb as parm7/prmtop file with boundary conditions
Gustaf Olsson
(Thu Nov 05 2020 - 03:17:09 PST)
[AMBER] Ambertools20 installation
Hrvoje Brkić
(Thu Nov 05 2020 - 07:31:41 PST)
Re: [AMBER] Ambertools20 installation
David A Case
(Thu Nov 05 2020 - 13:56:47 PST)
[AMBER] protein folding
h_sahakyan.mb.sci.am
(Thu Nov 05 2020 - 08:20:43 PST)
Re: [AMBER] protein folding
Carlos Simmerling
(Thu Nov 05 2020 - 08:38:04 PST)
[AMBER] Fwd: Re: protein folding
h_sahakyan.mb.sci.am
(Fri Nov 06 2020 - 06:02:34 PST)
[AMBER] using bridgebyatom keyword
Samuel Holmes
(Thu Nov 05 2020 - 10:22:47 PST)
Re: [AMBER] using bridgebyatom keyword
Daniel Roe
(Sat Nov 07 2020 - 04:54:43 PST)
[AMBER] installing pmemd.cuda (Amber20, WSL2)
Lucy Yang
(Thu Nov 05 2020 - 20:46:31 PST)
Re: [AMBER] installing pmemd.cuda (Amber20, WSL2)
Lucy Yang
(Thu Nov 05 2020 - 23:35:54 PST)
[AMBER] Help on understanding the errors
Ayesha Fatima
(Fri Nov 06 2020 - 00:23:22 PST)
Re: [AMBER] Help on understanding the errors
Dr. Anselm Horn
(Fri Nov 06 2020 - 02:48:47 PST)
Re: [AMBER] Help on understanding the errors
Ayesha Fatima
(Fri Nov 06 2020 - 03:02:13 PST)
Re: [AMBER] Help on understanding the errors
Bill Ross
(Fri Nov 06 2020 - 03:06:43 PST)
Re: [AMBER] Help on understanding the errors
Ayesha Fatima
(Fri Nov 06 2020 - 03:14:36 PST)
Re: [AMBER] Help on understanding the errors
Ayesha Fatima
(Fri Nov 06 2020 - 03:21:18 PST)
[AMBER] CPPTRAJ printout auto-detected hbond donor/acceptor
Gustaf Olsson
(Fri Nov 06 2020 - 01:24:28 PST)
Re: [AMBER] CPPTRAJ printout auto-detected hbond donor/acceptor
Daniel Roe
(Fri Nov 06 2020 - 05:53:37 PST)
Re: [AMBER] CPPTRAJ printout auto-detected hbond donor/acceptor
Gustaf Olsson
(Mon Nov 09 2020 - 00:40:53 PST)
Re: [AMBER] CPPTRAJ printout auto-detected hbond donor/acceptor
Gustaf Olsson
(Mon Nov 09 2020 - 00:45:26 PST)
Re: [AMBER] CPPTRAJ printout auto-detected hbond donor/acceptor
Daniel Roe
(Tue Nov 10 2020 - 06:26:32 PST)
Re: [AMBER] CPPTRAJ printout auto-detected hbond donor/acceptor
Gustaf Olsson
(Tue Nov 10 2020 - 23:46:37 PST)
[AMBER] protein domain "broken"
MYRIAN TORRES RICO
(Fri Nov 06 2020 - 02:45:06 PST)
Re: [AMBER] protein domain "broken"
Bill Ross
(Fri Nov 06 2020 - 03:03:02 PST)
Re: [AMBER] protein domain "broken"
MYRIAN TORRES RICO
(Fri Nov 06 2020 - 03:21:48 PST)
Re: [AMBER] protein domain "broken"
Dr. Anselm Horn
(Fri Nov 06 2020 - 03:49:45 PST)
Re: [AMBER] protein domain "broken"
MYRIAN TORRES RICO
(Fri Nov 06 2020 - 04:11:56 PST)
Re: [AMBER] protein domain "broken"
Carlos Simmerling
(Fri Nov 06 2020 - 04:12:02 PST)
Re: [AMBER] protein domain "broken"
MYRIAN TORRES RICO
(Fri Nov 06 2020 - 04:39:16 PST)
Re: [AMBER] protein domain "broken"
Dr. Anselm Horn
(Fri Nov 06 2020 - 08:05:07 PST)
Re: [AMBER] protein domain "broken"
MYRIAN TORRES RICO
(Mon Nov 09 2020 - 00:52:22 PST)
Re: [AMBER] protein domain "broken"
koushik kasavajhala
(Mon Nov 09 2020 - 00:53:57 PST)
Re: [AMBER] protein domain "broken"m
koushik kasavajhala
(Mon Nov 09 2020 - 00:59:00 PST)
Re: [AMBER] protein domain "broken"
koushik kasavajhala
(Mon Nov 09 2020 - 01:00:20 PST)
Re: [AMBER] protein domain "broken"
Dr. Anselm Horn
(Fri Nov 06 2020 - 03:03:22 PST)
Re: [AMBER] protein domain "broken"
MYRIAN TORRES RICO
(Fri Nov 06 2020 - 03:20:18 PST)
[AMBER] MMPBSA/GBSA
Manisha
(Fri Nov 06 2020 - 03:11:36 PST)
Re: [AMBER] MMPBSA/GBSA
Bill Ross
(Fri Nov 06 2020 - 03:18:14 PST)
[AMBER] FEW: Linear interaction energy calculations.
M RCC
(Fri Nov 06 2020 - 03:55:46 PST)
[AMBER] Protein preparation error
Ayesha Fatima
(Fri Nov 06 2020 - 08:05:23 PST)
Re: [AMBER] Protein preparation error
David A Case
(Fri Nov 06 2020 - 08:50:04 PST)
Re: [AMBER] Protein preparation error
Ayesha Fatima
(Fri Nov 06 2020 - 09:02:26 PST)
Re: [AMBER] Protein preparation error
Ayesha Fatima
(Fri Nov 06 2020 - 10:31:20 PST)
[AMBER] Discrepancy between interaction energy of amber coordinate trajectories of a system
Prathit Chatterjee
(Sat Nov 07 2020 - 05:19:17 PST)
Re: [AMBER] Discrepancy between interaction energy of amber coordinate trajectories of a system
Bill Ross
(Sat Nov 07 2020 - 05:28:00 PST)
Re: [AMBER] Discrepancy between interaction energy of amber coordinate trajectories of a system
Carlos Simmerling
(Sat Nov 07 2020 - 06:44:44 PST)
Re: [AMBER] Discrepancy between interaction energy of amber coordinate trajectories of a system
Prathit Chatterjee
(Sun Nov 08 2020 - 19:41:40 PST)
Re: [AMBER] Discrepancy between interaction energy of amber coordinate trajectories of a system
Carlos Simmerling
(Mon Nov 09 2020 - 06:51:55 PST)
[AMBER] AMORPHOUS HEMICELLULOSE
Pinky Mazumder
(Sat Nov 07 2020 - 10:22:44 PST)
[AMBER] Amber 20 on AMD ryzen + Nvidia 30XX
Jordi Bujons
(Sun Nov 08 2020 - 10:20:17 PST)
Re: [AMBER] Amber 20 on AMD ryzen + Nvidia 30XX
Robert Konecny
(Sun Nov 08 2020 - 13:08:59 PST)
Re: [AMBER] Amber 20 on AMD ryzen + Nvidia 30XX
Charo del Genio
(Sun Nov 08 2020 - 13:26:56 PST)
Re: [AMBER] Amber 20 on AMD ryzen + Nvidia 30XX
Raman Preet Singh
(Sun Nov 08 2020 - 23:20:57 PST)
Re: [AMBER] Amber 20 on AMD ryzen + Nvidia 30XX
Jordi Bujons
(Wed Nov 11 2020 - 05:47:18 PST)
Re: [AMBER] Amber 20 on AMD ryzen + Nvidia 30XX
Charo del Genio
(Fri Nov 13 2020 - 04:17:28 PST)
Re: [AMBER] Amber 20 on AMD ryzen + Nvidia 30XX
Jason Swails
(Thu Nov 19 2020 - 16:34:20 PST)
[AMBER] Addition of polyatomic ions in Leap
MADHUSMITA DEVI
(Sun Nov 08 2020 - 20:57:21 PST)
Re: [AMBER] Addition of polyatomic ions in Leap
David A Case
(Mon Nov 09 2020 - 05:40:09 PST)
Re: [AMBER] Addition of polyatomic ions in Leap
Bill Ross
(Mon Nov 09 2020 - 06:54:22 PST)
[AMBER] CPPTRAJ returns 'Warning: Box center specified but no box information'
Ikuo KURISAKI
(Mon Nov 09 2020 - 22:35:21 PST)
Re: [AMBER] CPPTRAJ returns 'Warning: Box center specified but no box information'
Daniel Roe
(Tue Nov 10 2020 - 06:20:54 PST)
[AMBER] iwrap/autoimage - analyses
Gustaf Olsson
(Tue Nov 10 2020 - 03:13:26 PST)
Re: [AMBER] iwrap/autoimage - analyses
Daniel Roe
(Tue Nov 10 2020 - 06:19:32 PST)
Re: [AMBER] iwrap/autoimage - analyses
Gustaf Olsson
(Wed Nov 11 2020 - 00:27:10 PST)
Re: [AMBER] Amber20 and RNA simulations
Piia Kokkonen
(Tue Nov 10 2020 - 04:38:25 PST)
[AMBER] FES (Ferredoxin) Amber Parameters
Maghsoud, Yazdan
(Tue Nov 10 2020 - 06:50:46 PST)
[AMBER] Query about generated (.pdb) files from GLYCAM Carbo builder
Pinky Mazumder
(Tue Nov 10 2020 - 11:51:59 PST)
Re: [AMBER] Query about generated (.pdb) files from GLYCAM Carbo builder
Gustaf Olsson
(Tue Nov 10 2020 - 23:51:49 PST)
Re: [AMBER] Help for building cross linking polymer using graphic antechamber
Pinky Mazumder
(Tue Nov 10 2020 - 19:06:02 PST)
Re: [AMBER] Help for building cross linking polymer using graphic antechamber
Gustaf Olsson
(Tue Nov 10 2020 - 23:56:21 PST)
Re: [AMBER] Help for building cross linking polymer using graphic antechamber
aishen
(Wed Nov 11 2020 - 00:27:39 PST)
[AMBER] error input
MYRIAN TORRES RICO
(Wed Nov 11 2020 - 04:31:12 PST)
Re: [AMBER] error input
David A Case
(Wed Nov 11 2020 - 05:44:02 PST)
Re: [AMBER] error input
MYRIAN TORRES RICO
(Wed Nov 11 2020 - 08:23:59 PST)
Re: [AMBER] error input
Carlos Simmerling
(Wed Nov 11 2020 - 08:35:16 PST)
Re: [AMBER] error input
David A Case
(Wed Nov 11 2020 - 19:30:32 PST)
Re: [AMBER] error input
MYRIAN TORRES RICO
(Thu Nov 12 2020 - 01:16:32 PST)
Re: [AMBER] error input
David A Case
(Thu Nov 12 2020 - 05:34:03 PST)
[AMBER] Changes in DNA sugar chilarity at NMR volume restrained simulation
lomzov
(Wed Nov 11 2020 - 21:45:02 PST)
Re: [AMBER] Changes in DNA sugar chilarity at NMR volume restrained simulation
David A Case
(Thu Nov 12 2020 - 05:27:06 PST)
[AMBER] TI-Amber
Ankita Tripathi
(Thu Nov 12 2020 - 05:19:31 PST)
Re: [AMBER] TI-Amber
Ankita Tripathi
(Sat Nov 14 2020 - 11:51:10 PST)
Re: [AMBER] TI-Amber
Giorgos Lambrinidis
(Sun Nov 15 2020 - 11:21:24 PST)
Re: [AMBER] TI-Amber
Ankita Tripathi
(Sun Nov 15 2020 - 11:31:58 PST)
Re: [AMBER] TI-Amber
Giorgos Lambrinidis
(Mon Nov 16 2020 - 00:18:42 PST)
Re: [AMBER] TI-Amber
Ankita Tripathi
(Tue Nov 17 2020 - 04:27:45 PST)
[AMBER] AMBER20, ff19SB and OPC
Kanin Wichapong
(Fri Nov 13 2020 - 02:57:49 PST)
Re: [AMBER] AMBER20, ff19SB and OPC
Stephan Schott
(Sat Nov 14 2020 - 10:20:43 PST)
Re: [AMBER] AMBER20, ff19SB and OPC
Liao
(Sat Nov 14 2020 - 11:07:40 PST)
Re: [AMBER] AMBER20, ff19SB and OPC
Carlos Simmerling
(Sat Nov 14 2020 - 10:38:52 PST)
Re: [AMBER] AMBER20, ff19SB and OPC
Carlos Simmerling
(Fri Nov 20 2020 - 04:24:18 PST)
[AMBER] How to correct the H atom direction in the HIE residue?
辛志宏
(Fri Nov 13 2020 - 05:41:02 PST)
Re: [AMBER] How to correct the H atom direction in the HIE residue?
Carlos Simmerling
(Fri Nov 13 2020 - 05:45:39 PST)
Re: [AMBER] How to correct the H atom direction in the HIE residue?
Song, Lin
(Fri Nov 13 2020 - 08:47:44 PST)
Re: [AMBER] How to correct the H atom direction in the HIE residue?
Abdul-Rashid III Sampaco
(Fri Nov 13 2020 - 10:32:27 PST)
Re: [AMBER] How to correct the H atom direction in the HIE residue?
Gustavo Seabra
(Fri Nov 13 2020 - 10:42:49 PST)
Re: [AMBER] How to correct the H atom direction in the HIE residue?
Carlos Simmerling
(Fri Nov 13 2020 - 10:47:23 PST)
Re: [AMBER] How to correct the H atom direction in the HIE residue?
Gustavo Seabra
(Fri Nov 13 2020 - 10:50:15 PST)
Re: [AMBER] How to correct the H atom direction in the HIE residue?
辛志宏
(Sat Nov 14 2020 - 05:24:07 PST)
[AMBER] Antechamber: Charge and dihedral issues
Salman Zarrini
(Fri Nov 13 2020 - 11:44:43 PST)
[AMBER] Fwd: Antechamber: Charge and dihedral issues
Salman Zarrini
(Sun Nov 15 2020 - 10:46:12 PST)
Re: [AMBER] Antechamber: Charge and dihedral issues
David A Case
(Mon Nov 16 2020 - 05:17:02 PST)
[AMBER] How to introduce repulsive force between ligands during simulation?
钟海洋
(Fri Nov 13 2020 - 23:49:58 PST)
[AMBER] GAFF.dat format: what does the second numeric column mean?
Zhu Liang
(Sat Nov 14 2020 - 09:35:40 PST)
Re: [AMBER] GAFF.dat format: what does the second numeric column mean?
Stephan Schott
(Sat Nov 14 2020 - 09:46:35 PST)
Re: [AMBER] GAFF.dat format: what does the second numeric column mean?
Zhu Liang
(Sat Nov 14 2020 - 10:58:05 PST)
[AMBER] MMPBSA.py bad atom type: M1 error
Vaibhav Dixit
(Mon Nov 16 2020 - 01:23:00 PST)
[AMBER] TI lambda scheduling file examples
Debarati DasGupta
(Mon Nov 16 2020 - 13:12:38 PST)
[AMBER] MCBP.py errors
Seibold, Steve Allan
(Mon Nov 16 2020 - 14:57:00 PST)
Re: [AMBER] MCBP.py errors
Pengfei Li
(Fri Nov 20 2020 - 08:13:53 PST)
[AMBER] thermal averaging of properties
Vaibhav Dixit
(Tue Nov 17 2020 - 18:58:11 PST)
Re: [AMBER] thermal averaging of properties
David A Case
(Wed Nov 18 2020 - 06:19:19 PST)
Re: [AMBER] thermal averaging of properties
Vaibhav Dixit
(Wed Nov 18 2020 - 06:24:34 PST)
[AMBER] FINAL RESULT MMPBSA QUERY
Manisha
(Tue Nov 17 2020 - 23:57:31 PST)
Re: [AMBER] FINAL RESULT MMPBSA QUERY
Ray Luo
(Wed Nov 18 2020 - 21:47:25 PST)
[AMBER] ABMD NFE queries
Victor Jun Yu Lim
(Wed Nov 18 2020 - 01:40:38 PST)
[AMBER] Unsupported Cuda Version on Amber 20 Installation
Setyanto Md
(Wed Nov 18 2020 - 03:57:36 PST)
Re: [AMBER] Unsupported Cuda Version on Amber 20 Installation
David A Case
(Wed Nov 18 2020 - 06:30:05 PST)
Re: [AMBER] Unsupported Cuda Version on Amber 20 Installation
viktor
(Wed Nov 18 2020 - 06:31:08 PST)
Re: [AMBER] Unsupported Cuda Version on Amber 20 Installation
Setyanto Md
(Thu Nov 19 2020 - 15:35:15 PST)
Re: [AMBER] Unsupported Cuda Version on Amber 20 Installation
David A Case
(Thu Nov 19 2020 - 18:24:01 PST)
Re: [AMBER] Unsupported Cuda Version on Amber 20 Installation
Setyanto Md
(Thu Nov 19 2020 - 20:08:29 PST)
Re: [AMBER] Unsupported Cuda Version on Amber 20 Installation
David A Case
(Fri Nov 20 2020 - 04:58:36 PST)
Re: [AMBER] Unsupported Cuda Version on Amber 20 Installation
Setyanto Md
(Fri Nov 20 2020 - 06:59:42 PST)
[AMBER] cpptraj donor/acceptor definitions
Gustaf Olsson
(Wed Nov 18 2020 - 04:42:45 PST)
Re: [AMBER] cpptraj donor/acceptor definitions
Daniel Roe
(Wed Nov 18 2020 - 06:06:44 PST)
Re: [AMBER] cpptraj donor/acceptor definitions
Gustaf Olsson
(Thu Nov 19 2020 - 02:46:00 PST)
Re: [AMBER] cpptraj donor/acceptor definitions
Daniel Roe
(Fri Nov 20 2020 - 08:13:27 PST)
Re: [AMBER] cpptraj donor/acceptor definitions
Gustaf Olsson
(Mon Nov 23 2020 - 00:11:56 PST)
Re: [AMBER] cpptraj donor/acceptor definitions
Daniel Roe
(Mon Nov 23 2020 - 05:50:11 PST)
Re: [AMBER] cpptraj donor/acceptor definitions
Gustaf Olsson
(Mon Nov 23 2020 - 06:25:26 PST)
Re: [AMBER] cpptraj donor/acceptor definitions
Gustaf Olsson
(Mon Nov 23 2020 - 06:51:37 PST)
Re: [AMBER] cpptraj donor/acceptor definitions
Daniel Roe
(Mon Nov 23 2020 - 06:56:08 PST)
Re: [AMBER] cpptraj donor/acceptor definitions
Gustaf Olsson
(Mon Nov 23 2020 - 08:22:49 PST)
[AMBER] pytraj
Pietro ARONICA
(Wed Nov 18 2020 - 09:03:45 PST)
Re: [AMBER] pytraj
Hai Nguyen
(Wed Nov 18 2020 - 16:26:28 PST)
Re: [AMBER] pytraj
Pietro ARONICA
(Wed Nov 18 2020 - 20:22:27 PST)
Re: [AMBER] pytraj
Hai Nguyen
(Thu Nov 19 2020 - 06:43:48 PST)
Re: [AMBER] pytraj
Pietro ARONICA
(Mon Nov 23 2020 - 02:16:28 PST)
Re: [AMBER] pytraj
Hai Nguyen
(Mon Nov 23 2020 - 10:28:51 PST)
Re: [AMBER] pytraj
Hai Nguyen
(Mon Nov 23 2020 - 10:47:07 PST)
[AMBER] How can I solve the high RMS problem?
변진영
(Wed Nov 18 2020 - 22:50:09 PST)
Re: [AMBER] How can I solve the high RMS problem?
David A Case
(Sun Nov 29 2020 - 10:45:07 PST)
[AMBER] jupyter notebook
aishen
(Wed Nov 18 2020 - 23:18:17 PST)
Re: [AMBER] jupyter notebook
Elvis Martis
(Thu Nov 19 2020 - 00:35:30 PST)
Re: [AMBER] jupyter notebook
Hai Nguyen
(Mon Nov 23 2020 - 17:59:56 PST)
[AMBER] Amber 18 GPU installation error
Nagakumar Bharatham
(Thu Nov 19 2020 - 00:56:13 PST)
Re: [AMBER] Amber 18 GPU installation error
Nagakumar Bharatham
(Sun Nov 22 2020 - 23:13:30 PST)
[AMBER] Ubuntu version compatible for gpu installation of AMBER 18
Jenny 148
(Thu Nov 19 2020 - 02:26:57 PST)
Re: [AMBER] Ubuntu version compatible for gpu installation of AMBER 18
aishen
(Thu Nov 19 2020 - 03:57:12 PST)
[AMBER] molecule twisted in QM/MM simulation
Qinghua Liao
(Thu Nov 19 2020 - 04:26:01 PST)
Re: [AMBER] molecule twisted in QM/MM simulation
David A Case
(Thu Nov 19 2020 - 08:00:25 PST)
Re: [AMBER] molecule twisted in QM/MM simulation
Qinghua Liao
(Sat Nov 21 2020 - 12:32:04 PST)
Re: [AMBER] molecule twisted in QM/MM simulation
Goetz, Andreas
(Sat Nov 21 2020 - 12:49:42 PST)
[AMBER] mdgx 'File not found' on macOS
h.jolon.icloud.com
(Thu Nov 19 2020 - 06:44:22 PST)
Re: [AMBER] mdgx 'File not found' on macOS
h.jolon.icloud.com
(Thu Nov 19 2020 - 06:52:32 PST)
[AMBER] tinker_to_amber
Michael Sonny Miller
(Thu Nov 19 2020 - 13:47:09 PST)
Re: [AMBER] tinker_to_amber
Emmett Leddin
(Wed Nov 25 2020 - 12:37:14 PST)
[AMBER] Question again
Paul Keller
(Thu Nov 19 2020 - 23:42:28 PST)
[AMBER] Amber 20 make install problem
Bruno Cramer
(Fri Nov 20 2020 - 06:13:41 PST)
Re: [AMBER] Amber 20 make install problem
David A Case
(Sat Nov 21 2020 - 05:39:53 PST)
Re: [AMBER] Prmtop for protein + 2 identical ligands has wrong dihedral parameters for the second ligand. LEaP bug?
Pengfei Li
(Fri Nov 20 2020 - 07:14:22 PST)
Re: [AMBER] a metal bound Met
Pengfei Li
(Fri Nov 20 2020 - 07:25:39 PST)
Re: [AMBER] a metal bound Met
Wu Xu
(Fri Nov 20 2020 - 07:55:42 PST)
Re: [AMBER] Problem with acpype
Pengfei Li
(Fri Nov 20 2020 - 08:37:36 PST)
Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"?
Liao
(Fri Nov 20 2020 - 13:18:33 PST)
Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"?
Carlos Simmerling
(Fri Nov 20 2020 - 14:29:53 PST)
Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"?
Liao
(Sun Nov 22 2020 - 16:20:43 PST)
Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"?
David A Case
(Sun Nov 22 2020 - 18:17:23 PST)
Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"?
Liao
(Sun Nov 22 2020 - 22:20:25 PST)
Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"?
Carlos Simmerling
(Mon Nov 23 2020 - 04:43:06 PST)
[AMBER] Regarding to the parameters setup in SMD simulation
辛志宏
(Sat Nov 21 2020 - 00:35:00 PST)
[AMBER] antechamber error -sqm.out missing
Bruno Cramer
(Sat Nov 21 2020 - 04:58:27 PST)
Re: [AMBER] antechamber error -sqm.out missing
David A Case
(Sat Nov 21 2020 - 05:53:17 PST)
[AMBER] Tail-to-tail peptide linker?
Alexander Izvorski
(Sat Nov 21 2020 - 21:53:50 PST)
Re: [AMBER] Tail-to-tail peptide linker?
David A Case
(Sun Nov 22 2020 - 05:57:30 PST)
[AMBER] phi cremer
MYRIAN TORRES RICO
(Mon Nov 23 2020 - 04:26:51 PST)
Re: [AMBER] phi cremer
Daniel Roe
(Wed Nov 25 2020 - 07:09:20 PST)
Re: [AMBER] phi cremer
MYRIAN TORRES RICO
(Wed Nov 25 2020 - 08:20:50 PST)
Re: [AMBER] phi cremer
Daniel Roe
(Fri Nov 27 2020 - 12:05:00 PST)
[AMBER] Installing AmberTools20 compile error
Lennart Gundelach
(Mon Nov 23 2020 - 22:55:45 PST)
Re: [AMBER] Installing AmberTools20 compile error
David A Case
(Tue Nov 24 2020 - 05:13:11 PST)
Re: [AMBER] Installing AmberTools20 compile error
Lennart Gundelach
(Wed Nov 25 2020 - 04:47:32 PST)
[AMBER] MMPBSA.py: "fork()" system call to create a child process
Lennart Gundelach
(Mon Nov 23 2020 - 23:02:44 PST)
Re: [AMBER] MMPBSA.py: "fork()" system call to create a child process
David A Case
(Tue Nov 24 2020 - 07:52:02 PST)
[AMBER] phi angle puckering
MYRIAN TORRES RICO
(Tue Nov 24 2020 - 00:45:52 PST)
[AMBER] System blows up when simulating under npt
Amit Sharma (Asstt. Prof., MCARS)
(Tue Nov 24 2020 - 03:04:38 PST)
Re: [AMBER] System blows up when simulating under npt
Carlos Simmerling
(Tue Nov 24 2020 - 03:09:42 PST)
Re: [AMBER] System blows up when simulating under npt
Juraj Dobias
(Tue Nov 24 2020 - 03:35:06 PST)
Re: [AMBER] System blows up when simulating under npt
Amit Sharma (Asstt. Prof., MCARS)
(Tue Nov 24 2020 - 03:44:21 PST)
Re: [AMBER] System blows up when simulating under npt
Carlos Simmerling
(Tue Nov 24 2020 - 04:41:13 PST)
Re: [AMBER] System blows up when simulating under npt
Daniel Roe
(Wed Nov 25 2020 - 07:12:26 PST)
Re: [AMBER] System blows up when simulating under npt
Carlos Simmerling
(Wed Nov 25 2020 - 07:18:07 PST)
[AMBER] Using the rep.C0.pdb as a reference structure in RMSD analysis
Soheila Shokrollahzade
(Tue Nov 24 2020 - 07:56:42 PST)
Re: [AMBER] Using the rep.C0.pdb as a reference structure in RMSD analysis
Daniel Roe
(Wed Nov 25 2020 - 07:18:33 PST)
[AMBER] Help in amber TI automation script
Delwakkada Liyanage, Senal Dinuka
(Tue Nov 24 2020 - 12:29:52 PST)
Re: [AMBER] NOE analysis with cpptraj
Daniel Roe
(Wed Nov 25 2020 - 07:24:11 PST)
[AMBER] Fwd: System blows up when simulating under npt
Amit Sharma (Asstt. Prof., MCARS)
(Wed Nov 25 2020 - 09:15:47 PST)
Re: [AMBER] Fwd: System blows up when simulating under npt
Carlos Simmerling
(Wed Nov 25 2020 - 09:21:19 PST)
Re: [AMBER] Fwd: System blows up when simulating under npt
Bill Ross
(Wed Nov 25 2020 - 18:12:04 PST)
[AMBER] AMBER 18 cuda installation error
Mariangela Dametto
(Wed Nov 25 2020 - 11:24:35 PST)
Re: [AMBER] AMBER 18 cuda installation error
Tru Huynh
(Wed Nov 25 2020 - 14:40:24 PST)
Re: [AMBER] AMBER 18 cuda installation error
David A Case
(Fri Nov 27 2020 - 05:14:08 PST)
Re: [AMBER] AMBER 18 cuda installation error
Mariangela Dametto
(Mon Nov 30 2020 - 04:25:25 PST)
Re: [AMBER] AMBER 18 cuda installation error
accuratefreeenergy.gmail.com
(Mon Nov 30 2020 - 05:06:20 PST)
[AMBER] Antechamber permissions issue
Sam Walsworth (Researcher)
(Thu Nov 26 2020 - 09:37:18 PST)
Re: [AMBER] Antechamber permissions issue
David A Case
(Fri Nov 27 2020 - 04:57:29 PST)
Re: [AMBER] Antechamber permissions issue
Sam Walsworth (Researcher)
(Fri Nov 27 2020 - 06:37:44 PST)
Re: [AMBER] Antechamber permissions issue
David A Case
(Fri Nov 27 2020 - 14:10:34 PST)
Re: [AMBER] Antechamber permissions issue
Sam Walsworth (Researcher)
(Mon Nov 30 2020 - 02:22:36 PST)
Re: [AMBER] Antechamber permissions issue
Sam Walsworth (Researcher)
(Mon Nov 30 2020 - 02:48:13 PST)
Re: [AMBER] Antechamber permissions issue
Sam Walsworth (Researcher)
(Mon Nov 30 2020 - 03:23:56 PST)
[AMBER] Partial Charge with RESP (antechamber)
Michele Vanini
(Thu Nov 26 2020 - 09:53:57 PST)
Re: [AMBER] Partial Charge with RESP (antechamber)
David Cerutti
(Thu Nov 26 2020 - 18:24:54 PST)
Re: [AMBER] Partial Charge with RESP (antechamber)
Dr. Anselm Horn
(Fri Nov 27 2020 - 00:36:54 PST)
Re: [AMBER] Partial Charge with RESP (antechamber)
Michele Vanini
(Fri Nov 27 2020 - 01:12:37 PST)
[AMBER] An error during NPT/production (GPU run)
Женя Елизарова
(Thu Nov 26 2020 - 10:05:33 PST)
Re: [AMBER] An error during NPT/production (GPU run)
David A Case
(Fri Nov 27 2020 - 05:04:41 PST)
Re: [AMBER] An error during NPT/production (GPU run)
Женя Елизарова
(Sat Nov 28 2020 - 00:10:09 PST)
Re: [AMBER] An error during NPT/production (GPU run)
David A Case
(Sun Nov 29 2020 - 10:39:39 PST)
Re: [AMBER] An error during NPT/production (GPU run)
Женя Елизарова
(Sun Nov 29 2020 - 22:09:24 PST)
[AMBER] md simulation error
Kehinde Idowu
(Fri Nov 27 2020 - 08:41:08 PST)
Re: [AMBER] md simulation error
David A Case
(Fri Nov 27 2020 - 14:14:23 PST)
Re: [AMBER] md simulation error
Kehinde Idowu
(Sat Nov 28 2020 - 11:34:22 PST)
Re: [AMBER] md simulation error
David A Case
(Sun Nov 29 2020 - 10:19:59 PST)
[AMBER] AMBER20 TI calculations
Debarati DasGupta
(Fri Nov 27 2020 - 09:15:49 PST)
Re: [AMBER] AMBER20 TI calculations
Adrian Roitberg
(Fri Nov 27 2020 - 09:21:09 PST)
[AMBER] FW: AMBER20 TI calculations
Debarati DasGupta
(Fri Nov 27 2020 - 09:52:37 PST)
[AMBER] fail when run pmem.cuda
Carlos
(Sat Nov 28 2020 - 01:04:07 PST)
Re: [AMBER] fail when run pmem.cuda
David A Case
(Sun Nov 29 2020 - 10:35:13 PST)
Re: [AMBER] fail when run pmem.cuda
Carlos
(Sun Nov 29 2020 - 21:56:43 PST)
[AMBER] Effective Way To Perform Molecular Dynamics Simulation
Erdem Yeler
(Sat Nov 28 2020 - 15:20:56 PST)
Re: [AMBER] Effective Way To Perform Molecular Dynamics Simulation
Carlos Simmerling
(Sun Nov 29 2020 - 03:32:53 PST)
[AMBER] question about gaps
Gordon Richard Chalmers
(Sat Nov 28 2020 - 19:43:05 PST)
Re: [AMBER] question about gaps
David A Case
(Sun Nov 29 2020 - 10:26:03 PST)
Re: [AMBER] question about gaps
Gordon Richard Chalmers
(Sun Nov 29 2020 - 10:41:30 PST)
[AMBER] TI electrostatic free energy
Franz Waibl
(Mon Nov 30 2020 - 06:34:44 PST)
Re: [AMBER] TI electrostatic free energy
David A Case
(Mon Nov 30 2020 - 10:10:18 PST)
Last message date
:
Mon Nov 30 2020 - 10:30:02 PST
Archived on
: Mon Nov 25 2024 - 05:55:55 PST
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