Amber Archive Jan 2020 by thread
335 messages
:
Starting
Wed Jan 01 2020 - 13:30:02 PST,
Ending
Fri Jan 31 2020 - 12:00:02 PST
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Re: [AMBER] Tleap naming problem
Rui Chen
(Wed Jan 01 2020 - 13:19:00 PST)
Re: [AMBER] Tleap naming problem
David Case
(Thu Jan 02 2020 - 05:30:41 PST)
[AMBER] ligand clustering
Neha Gandhi
(Wed Jan 01 2020 - 21:47:51 PST)
[AMBER] Regarding clustering using mmtsb toolkit
Sruthi Sudhakar
(Wed Jan 01 2020 - 22:37:22 PST)
Re: [AMBER] Regarding clustering using mmtsb toolkit
Carlos Simmerling
(Thu Jan 02 2020 - 04:58:17 PST)
Re: [AMBER] Regarding clustering using mmtsb toolkit
David Case
(Thu Jan 02 2020 - 05:35:57 PST)
[AMBER] NMR distance restrained MD
maya nair
(Wed Jan 01 2020 - 23:56:32 PST)
Re: [AMBER] NMR distance restrained MD
David Case
(Thu Jan 02 2020 - 05:41:00 PST)
Re: [AMBER] NMR distance restrained MD
maya nair
(Mon Jan 06 2020 - 04:21:57 PST)
Re: [AMBER] NMR distance restrained MD
Christina Bergonzo
(Thu Jan 02 2020 - 05:45:30 PST)
Re: [AMBER] NMR distance restrained MD
maya nair
(Mon Jan 06 2020 - 04:17:14 PST)
Re: [AMBER] NMR distance restrained MD
maya nair
(Tue Jan 28 2020 - 23:44:59 PST)
[AMBER] query
ankita mehta
(Thu Jan 02 2020 - 08:45:08 PST)
Re: [AMBER] query
David Case
(Thu Jan 02 2020 - 12:13:55 PST)
Re: [AMBER] query
ankita mehta
(Fri Jan 03 2020 - 02:50:20 PST)
[AMBER] MMPBSA error
Rui Chen
(Thu Jan 02 2020 - 16:27:54 PST)
Re: [AMBER] MMPBSA error
Ray Luo
(Thu Jan 02 2020 - 16:37:15 PST)
Re: [AMBER] MMPBSA error
Rui Chen
(Thu Jan 02 2020 - 21:37:14 PST)
Re: [AMBER] MMPBSA error
Ray Luo
(Thu Jan 02 2020 - 22:15:58 PST)
Re: [AMBER] MMPBSA error
Rui Chen
(Fri Jan 03 2020 - 08:58:42 PST)
Re: [AMBER] MMPBSA error
Ray Luo
(Fri Jan 03 2020 - 12:05:06 PST)
Re: [AMBER] MMPBSA error
Rui Chen
(Fri Jan 03 2020 - 12:59:10 PST)
Re: [AMBER] MMPBSA error
Ray Luo
(Sat Jan 04 2020 - 17:41:50 PST)
[AMBER] Semi-empirical QMMD on all molecules
Abdullah Faheem
(Thu Jan 02 2020 - 23:43:39 PST)
Re: [AMBER] Semi-empirical QMMD on all molecules
Goetz, Andreas
(Fri Jan 03 2020 - 03:36:43 PST)
[AMBER] Query
ankita mehta
(Fri Jan 03 2020 - 02:42:39 PST)
[AMBER] Drug parameter generation
Madhur Aggarwal
(Fri Jan 03 2020 - 10:09:16 PST)
Re: [AMBER] Drug parameter generation
Carlos Simmerling
(Fri Jan 03 2020 - 10:22:19 PST)
[AMBER] Glycosylation issue: Atom xx was assigned a lower molecule # than previous atom.
zizhang sheng
(Fri Jan 03 2020 - 13:44:04 PST)
Re: [AMBER] Glycosylation issue: Atom xx was assigned a lower molecule # than previous atom.
Lachele Foley
(Fri Jan 03 2020 - 14:44:14 PST)
Re: [AMBER] Glycosylation issue: Atom xx was assigned a lower molecule # than previous atom.
zz sheng
(Fri Jan 03 2020 - 15:43:14 PST)
Re: [AMBER] Glycosylation issue: Atom xx was assigned a lower molecule # than previous atom.
Lachele Foley
(Fri Jan 03 2020 - 15:49:35 PST)
[AMBER] esp charge
Rui Chen
(Fri Jan 03 2020 - 16:49:52 PST)
[AMBER] Problems using groups to provide centre for solvent caps in tLeap
David Wright
(Sat Jan 04 2020 - 05:10:03 PST)
[AMBER] Fwd: Problems using groups to provide centre for solvent caps in tLeap
David Wright
(Mon Jan 06 2020 - 03:37:59 PST)
Re: [AMBER] Fwd: Problems using groups to provide centre for solvent caps in tLeap
David Case
(Mon Jan 06 2020 - 06:34:20 PST)
Re: [AMBER] Fwd: Problems using groups to provide centre for solvent caps in tLeap
David Wright
(Tue Jan 07 2020 - 03:41:40 PST)
[AMBER] parmed issue
Ayesha Fatima
(Sat Jan 04 2020 - 05:50:11 PST)
Re: [AMBER] parmed issue
David Case
(Sat Jan 04 2020 - 14:16:27 PST)
[AMBER] hiii
ankita mehta
(Sat Jan 04 2020 - 05:54:40 PST)
Re: [AMBER] hiii
David Case
(Sat Jan 04 2020 - 14:18:12 PST)
[AMBER] hiiiiii
ankita mehta
(Sat Jan 04 2020 - 07:17:42 PST)
[AMBER] hiiiii
ankita mehta
(Sat Jan 04 2020 - 23:01:39 PST)
Re: [AMBER] hiiiii
David Case
(Sun Jan 05 2020 - 05:47:26 PST)
[AMBER] pmemd.cuda:command not found
Sruthi Sudhakar
(Sat Jan 04 2020 - 23:28:32 PST)
Re: [AMBER] pmemd.cuda:command not found
Liao
(Sat Jan 04 2020 - 23:56:35 PST)
[AMBER] MMPBSA standard deviation (Geng Dong)
东庚
(Sun Jan 05 2020 - 03:30:01 PST)
Re: [AMBER] MMPBSA standard deviation (Geng Dong)
Ray Luo
(Sun Jan 05 2020 - 07:46:29 PST)
[AMBER] hiiiii
ankita mehta
(Sun Jan 05 2020 - 06:18:43 PST)
Re: [AMBER] hiiiii
Carlos Simmerling
(Sun Jan 05 2020 - 06:32:56 PST)
Re: [AMBER] hiiiii
ankita mehta
(Sun Jan 05 2020 - 07:20:44 PST)
Re: [AMBER] hiiiii
Carlos Simmerling
(Sun Jan 05 2020 - 07:28:38 PST)
Re: [AMBER] hiiiii
ankita mehta
(Sun Jan 05 2020 - 07:37:54 PST)
Re: [AMBER] hiiiii
David Case
(Sun Jan 05 2020 - 10:32:44 PST)
Re: [AMBER] hiiiii
ankita mehta
(Sun Jan 05 2020 - 20:02:52 PST)
Re: [AMBER] hiiiii
Cory Ayres
(Mon Jan 06 2020 - 03:19:12 PST)
Re: [AMBER] hiiiii
ankita mehta
(Sun Jan 05 2020 - 23:43:51 PST)
[AMBER] gaff with and without gaff atom types
Erdem Yeler
(Sun Jan 05 2020 - 08:32:08 PST)
Re: [AMBER] gaff with and without gaff atom types
David Case
(Sun Jan 05 2020 - 10:42:28 PST)
Re: [AMBER] gaff with and without gaff atom types
Erdem Yeler
(Tue Jan 07 2020 - 00:27:24 PST)
[AMBER] Molecule is wrapped out of the cell.
Petro
(Mon Jan 06 2020 - 02:44:51 PST)
Re: [AMBER] Molecule is wrapped out of the cell.
David Case
(Mon Jan 06 2020 - 07:07:43 PST)
Re: [AMBER] Molecule is wrapped out of the cell.
Petro
(Tue Jan 07 2020 - 09:32:41 PST)
[AMBER] Umbrella sampling sufficient overlap test
Martin Rosellen
(Mon Jan 06 2020 - 04:20:06 PST)
Re: [AMBER] empty cein file redox potential calculations
Vaibhav Dixit
(Mon Jan 06 2020 - 00:59:37 PST)
Re: [AMBER] empty cein file redox potential calculations
Cruzeiro,Vinicius Wilian D
(Thu Jan 09 2020 - 07:01:11 PST)
[AMBER] printing charges in pdb
Vaibhav Dixit
(Mon Jan 06 2020 - 01:44:53 PST)
Re: [AMBER] printing charges in pdb
David Case
(Mon Jan 06 2020 - 07:04:07 PST)
Re: [AMBER] printing charges in pdb
Vaibhav Dixit
(Mon Jan 06 2020 - 09:04:05 PST)
[AMBER] Any help on the error
Debarati DasGupta
(Mon Jan 06 2020 - 12:22:52 PST)
[AMBER] Amber 18 installation error
Billiot, Eugene
(Mon Jan 06 2020 - 14:29:11 PST)
Re: [AMBER] Amber 18 installation error
David Case
(Tue Jan 07 2020 - 06:09:08 PST)
Re: [AMBER] Amber 18 installation error
Billiot, Eugene
(Tue Jan 07 2020 - 09:19:04 PST)
Re: [AMBER] Any help on the error
David Case
(Tue Jan 07 2020 - 05:59:45 PST)
[AMBER] [ Lone pair electron & Polymer ]
조준범
(Mon Jan 06 2020 - 22:06:13 PST)
[AMBER] [ Polymer with Extra Points ]
조준범
(Mon Jan 06 2020 - 22:40:38 PST)
Re: [AMBER] [ Polymer with Extra Points ]
David Cerutti
(Mon Jan 06 2020 - 23:56:54 PST)
Re: [AMBER] [ Polymer with Extra Points ]
조준범
(Tue Jan 07 2020 - 01:04:40 PST)
Re: [AMBER] [ Polymer with Extra Points ]
David Cerutti
(Thu Jan 09 2020 - 00:02:47 PST)
Re: [AMBER] [ Polymer with Extra Points ]
조준범
(Thu Jan 09 2020 - 21:29:10 PST)
[AMBER] DOPC lipid bilayer deformation in Implicit MD simulation using Lipid14 force field in Amber18
Bhat Zahoor
(Mon Jan 06 2020 - 23:16:55 PST)
Re: [AMBER] DOPC lipid bilayer deformation in Implicit MD simulation using Lipid14 force field in Amber18
Gould, Ian R
(Tue Jan 07 2020 - 00:37:25 PST)
[AMBER] Glycoprotein MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest
zizhang sheng
(Tue Jan 07 2020 - 07:47:45 PST)
[AMBER] TI data collection of DU/Dlambda at constant volume
Debarati DasGupta
(Tue Jan 07 2020 - 09:00:20 PST)
[AMBER] P2 correlation functions questions
erik zuiderweg
(Tue Jan 07 2020 - 09:08:28 PST)
Re: [AMBER] P2 correlation functions questions
David Case
(Tue Jan 07 2020 - 18:29:27 PST)
[AMBER] saxs
Adrian Roitberg
(Tue Jan 07 2020 - 12:41:25 PST)
Re: [AMBER] AMBER 18 cuda installation
David Case
(Tue Jan 07 2020 - 18:47:26 PST)
[AMBER] Question about addtobox
Petro
(Tue Jan 07 2020 - 22:28:09 PST)
Re: [AMBER] Question about addtobox
David Case
(Wed Jan 08 2020 - 07:22:21 PST)
Re: [AMBER] Question about addtobox
Petro
(Wed Jan 08 2020 - 15:19:41 PST)
Re: [AMBER] Question about addtobox
David Cerutti
(Thu Jan 09 2020 - 06:52:13 PST)
Re: [AMBER] Question about addtobox
David Case
(Thu Jan 09 2020 - 10:03:14 PST)
[AMBER] Adjacent cell molecules appear in the trajectory after autoimaging in cpptraj [ DOPC lipid bilayer simulation with lipid14 force field]
Bhat Zahoor
(Wed Jan 08 2020 - 01:46:26 PST)
[AMBER] Generalized Born and entropy
Martin Rosellen
(Wed Jan 08 2020 - 06:03:51 PST)
Re: [AMBER] Generalized Born and entropy
David Case
(Wed Jan 08 2020 - 07:30:25 PST)
Re: [AMBER] Generalized Born and entropy
Rosellen, Martin
(Mon Jan 13 2020 - 04:48:19 PST)
Re: [AMBER] Generalized Born and entropy
Carlos Simmerling
(Mon Jan 13 2020 - 05:04:43 PST)
Re: [AMBER] error
MYRIAN TORRES RICO
(Wed Jan 08 2020 - 07:07:38 PST)
Re: [AMBER] error
Gustaf Olsson
(Wed Jan 08 2020 - 22:54:22 PST)
[AMBER] saxs_md
Buteler,Maria del Pilar
(Wed Jan 08 2020 - 08:49:02 PST)
Re: [AMBER] saxs_md
Christina Bergonzo
(Wed Jan 08 2020 - 09:25:11 PST)
[AMBER] NPT density equilibration
Debarati DasGupta
(Wed Jan 08 2020 - 12:43:00 PST)
[AMBER] FW: NPT density equilibration
Debarati DasGupta
(Wed Jan 08 2020 - 12:44:41 PST)
[AMBER] [ Polymer ] Parameter Modification
조준범
(Wed Jan 08 2020 - 21:17:32 PST)
Re: [AMBER] [ Polymer ] Parameter Modification
David Cerutti
(Wed Jan 08 2020 - 21:56:12 PST)
[AMBER] Resolving overlapping atoms.
Petro
(Thu Jan 09 2020 - 01:54:12 PST)
Re: [AMBER] Resolving overlapping atoms.
David Case
(Thu Jan 09 2020 - 06:23:04 PST)
Re: [AMBER] Resolving overlapping atoms.
Petro
(Thu Jan 09 2020 - 10:19:36 PST)
[AMBER] charting Ligand's movement in the binding pocket
Prasanth G, Research Scholar
(Thu Jan 09 2020 - 02:58:01 PST)
Re: [AMBER] charting Ligand's movement in the binding pocket
Markowska
(Thu Jan 09 2020 - 12:02:08 PST)
[AMBER] [ inpcrd file ]
조준범
(Thu Jan 09 2020 - 03:09:29 PST)
Re: [AMBER] [ inpcrd file ]
Gustaf Olsson
(Thu Jan 09 2020 - 03:40:35 PST)
[AMBER] Lipid bilayer imaging problem
Bhat Zahoor
(Thu Jan 09 2020 - 03:58:07 PST)
Re: [AMBER] Lipid bilayer imaging problem
Chetna Tyagi
(Thu Jan 09 2020 - 03:48:47 PST)
Re: [AMBER] Lipid bilayer imaging problem
Bhat Zahoor
(Thu Jan 09 2020 - 04:59:41 PST)
[AMBER] MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest
zizhang sheng
(Thu Jan 09 2020 - 06:18:32 PST)
Re: [AMBER] MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest
David Case
(Thu Jan 09 2020 - 10:01:48 PST)
Re: [AMBER] MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest
zizhang sheng
(Fri Jan 10 2020 - 09:29:32 PST)
Re: [AMBER] MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest
David Case
(Fri Jan 10 2020 - 12:54:26 PST)
Re: [AMBER] MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest
zizhang sheng
(Fri Jan 10 2020 - 13:43:01 PST)
[AMBER] weights for the lambda values
Debarati DasGupta
(Thu Jan 09 2020 - 11:30:49 PST)
Re: [AMBER] weights for the lambda values
Carlos Simmerling
(Fri Jan 10 2020 - 03:30:35 PST)
[AMBER] Cpptraj - Density Action Command Units
An Ta
(Thu Jan 09 2020 - 13:11:53 PST)
[AMBER] [ prmtop ] SOLVENT_POINTERS
조준범
(Thu Jan 09 2020 - 21:15:18 PST)
Re: [AMBER] [ prmtop ] SOLVENT_POINTERS
Carlos Simmerling
(Fri Jan 10 2020 - 03:31:25 PST)
[AMBER] [ Error with MD ] Energetics of the system
조준범
(Thu Jan 09 2020 - 23:35:38 PST)
Re: [AMBER] [ Error with MD ] Energetics of the system
David Case
(Fri Jan 10 2020 - 05:43:39 PST)
[AMBER] Is minimization and equilibration needed in umbrella sampling?
Qing Lv
(Fri Jan 10 2020 - 07:46:29 PST)
[AMBER] Is NPT ensemble necessary for the protein-water system?
Qing Lv
(Fri Jan 10 2020 - 07:55:57 PST)
[AMBER] Is error bar necessary for umbrella sampling?
Qing Lv
(Mon Jan 13 2020 - 06:36:15 PST)
Re: [AMBER] Is error bar necessary for umbrella sampling?
Carlos Simmerling
(Mon Jan 13 2020 - 06:42:49 PST)
Re: [AMBER] Is error bar necessary for umbrella sampling?
Qing Lv
(Mon Jan 13 2020 - 18:48:06 PST)
Re: [AMBER] Is error bar necessary for umbrella sampling?
Carlos Simmerling
(Tue Jan 14 2020 - 03:30:35 PST)
[AMBER] ff99SBnmr2 Force field implemented in AMBER18
Lod King
(Fri Jan 10 2020 - 17:41:14 PST)
Re: [AMBER] ff99SBnmr2 Force field implemented in AMBER18
Carlos Simmerling
(Fri Jan 10 2020 - 17:58:30 PST)
[AMBER] Tracking ligand position throughout equilibration stages
Debarati DasGupta
(Sat Jan 11 2020 - 07:21:37 PST)
Re: [AMBER] Tracking ligand position throughout equilibration stages
Dr. Anselm Horn
(Mon Jan 13 2020 - 01:34:40 PST)
Re: [AMBER] Tracking ligand position throughout equilibration stages
Carlos Simmerling
(Mon Jan 13 2020 - 02:29:32 PST)
[AMBER] Custom language module(s) for AMBER file types for common text editors?
Makay Murray
(Sat Jan 11 2020 - 18:17:06 PST)
Re: [AMBER] Custom language module(s) for AMBER file types for common text editors?
Matias Machado
(Wed Jan 15 2020 - 12:23:52 PST)
[AMBER] installing amber on wsl
Ayesha Fatima
(Sun Jan 12 2020 - 05:29:26 PST)
Re: [AMBER] installing amber on wsl
David Case
(Sun Jan 12 2020 - 11:56:35 PST)
Re: [AMBER] installing amber on wsl
Ayesha Fatima
(Sun Jan 12 2020 - 22:54:28 PST)
Re: [AMBER] installing amber on wsl
Ayesha Fatima
(Mon Jan 13 2020 - 06:59:49 PST)
Re: [AMBER] installing amber on wsl
ALAMGIR KHAN
(Sun Jan 12 2020 - 20:04:17 PST)
[AMBER] [ MD Failure ]
조준범
(Sun Jan 12 2020 - 08:19:33 PST)
Re: [AMBER] [ MD Failure ]
David Case
(Mon Jan 13 2020 - 06:27:42 PST)
[AMBER] compatible graphics card
Antonio Bauzá
(Sun Jan 12 2020 - 09:01:29 PST)
[AMBER] Fwd: Periodic box problem when simulating Membrane system
Tiejun Wei
(Mon Jan 13 2020 - 06:26:41 PST)
Re: [AMBER] Periodic box problem when simulating Membrane system
Gustaf Olsson
(Mon Jan 13 2020 - 06:44:36 PST)
Re: [AMBER] Periodic box problem when simulating Membrane system
Bhat Zahoor
(Mon Jan 13 2020 - 07:09:40 PST)
[AMBER] CPPTRAJ-Hbonds
Rui Chen
(Mon Jan 13 2020 - 07:49:11 PST)
Re: [AMBER] CPPTRAJ-Hbonds
Daniel Roe
(Mon Jan 13 2020 - 09:08:01 PST)
[AMBER] parameters for Si3N4
Akshay Prabhakant
(Mon Jan 13 2020 - 08:38:24 PST)
[AMBER] Error with using dpeaks clustering in CPPTRAJ
yinglong.miao.gmail.com
(Mon Jan 13 2020 - 15:50:49 PST)
Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ
Daniel Roe
(Mon Jan 13 2020 - 16:20:42 PST)
Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ
Yinglong Miao
(Mon Jan 13 2020 - 17:10:04 PST)
Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ
Daniel Roe
(Tue Jan 14 2020 - 07:46:30 PST)
Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ
Yinglong Miao
(Tue Jan 14 2020 - 08:05:11 PST)
Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ
yinglong.miao.gmail.com
(Tue Jan 14 2020 - 09:34:22 PST)
Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ
Daniel Roe
(Fri Jan 17 2020 - 06:34:12 PST)
Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ
Daniel Roe
(Fri Jan 17 2020 - 06:37:12 PST)
Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ
Daniel Roe
(Fri Jan 17 2020 - 06:41:09 PST)
Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ
Yinglong Miao
(Fri Jan 17 2020 - 07:09:34 PST)
Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ
Daniel Roe
(Fri Jan 17 2020 - 07:35:57 PST)
Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ
Yinglong Miao
(Fri Jan 17 2020 - 07:45:10 PST)
[AMBER] ligand split
MYRIAN TORRES RICO
(Tue Jan 14 2020 - 09:07:35 PST)
Re: [AMBER] ligand split
David Case
(Tue Jan 14 2020 - 11:25:48 PST)
Re: [AMBER] ligand split
MYRIAN TORRES RICO
(Wed Jan 15 2020 - 02:26:22 PST)
Re: [AMBER] ligand split
Carlos Simmerling
(Wed Jan 15 2020 - 02:31:48 PST)
Re: [AMBER] ligand split
MYRIAN TORRES RICO
(Wed Jan 15 2020 - 02:44:40 PST)
Re: [AMBER] ligand split
Carlos Simmerling
(Wed Jan 15 2020 - 03:07:00 PST)
Re: [AMBER] ligand split
MYRIAN TORRES RICO
(Wed Jan 15 2020 - 04:52:20 PST)
Re: [AMBER] ligand split
Carlos Simmerling
(Wed Jan 15 2020 - 10:22:33 PST)
Re: [AMBER] ligand split
MYRIAN TORRES RICO
(Fri Jan 17 2020 - 07:15:52 PST)
Re: [AMBER] ligand split
Carlos Simmerling
(Fri Jan 17 2020 - 07:24:07 PST)
Re: [AMBER] ligand split
MYRIAN TORRES RICO
(Fri Jan 17 2020 - 07:32:27 PST)
[AMBER] modeling a Schiff base with GAFF atom types
Sally Pias
(Tue Jan 14 2020 - 15:16:57 PST)
Re: [AMBER] modeling a Schiff base with GAFF atom types
David Case
(Wed Jan 15 2020 - 05:54:42 PST)
Re: [AMBER] Generating parameters for iron-sulfur protein
Baker, Joseph
(Tue Jan 14 2020 - 20:51:28 PST)
Re: [AMBER] Generating parameters for iron-sulfur protein
Pengfei Li
(Sat Jan 18 2020 - 16:39:57 PST)
[AMBER] RESP fitting
Sruthi Sudhakar
(Wed Jan 15 2020 - 04:58:56 PST)
Re: [AMBER] RESP fitting
Elvis Martis
(Wed Jan 15 2020 - 04:53:12 PST)
[AMBER] How to use polarizable water model in Amber 18?
Markowska
(Wed Jan 15 2020 - 05:39:39 PST)
Re: [AMBER] How to use polarizable water model in Amber 18?
Matias Machado
(Wed Jan 15 2020 - 08:46:11 PST)
Re: [AMBER] How to use polarizable water model in Amber 18?
Carlos Simmerling
(Wed Jan 15 2020 - 10:23:48 PST)
Re: [AMBER] How to use polarizable water model in Amber 18?
Markowska
(Fri Jan 17 2020 - 00:22:11 PST)
Re: [AMBER] How to use polarizable water model in Amber 18?
Markowska
(Sat Jan 18 2020 - 10:01:14 PST)
Re: [AMBER] How to use polarizable water model in Amber 18?
David Case
(Sun Jan 19 2020 - 17:46:57 PST)
[AMBER] Harmless bug in Lipid11-17 residue libraries causing tleap to split fragments in saved PDB
Matias Machado
(Wed Jan 15 2020 - 08:32:38 PST)
[AMBER] Membrane simulation with PSM
cpimenta
(Wed Jan 15 2020 - 11:09:24 PST)
[AMBER] ValueError: could not convert string to float: ********* Error occured on rank 0. Exiting. All files have been retained.
Neha Gandhi
(Wed Jan 15 2020 - 20:35:09 PST)
Re: [AMBER] ValueError: could not convert string to float: ********* Error occured on rank 0. Exiting. All files have been retained.
David Case
(Thu Jan 16 2020 - 05:36:00 PST)
[AMBER] Reg. Centering of Molecule and Periodic Boundary Conditions
DHEERAJ CHITARA
(Thu Jan 16 2020 - 00:46:32 PST)
Re: [AMBER] Reg. Centering of Molecule and Periodic Boundary Conditions
Daniel Roe
(Thu Jan 16 2020 - 12:26:02 PST)
[AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer
Casalini Tommaso
(Thu Jan 16 2020 - 01:30:58 PST)
Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer
Stephan Schott
(Thu Jan 16 2020 - 04:13:59 PST)
Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer
Casalini Tommaso
(Thu Jan 16 2020 - 04:37:26 PST)
Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer
Stephan Schott
(Thu Jan 16 2020 - 14:37:43 PST)
Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer
Casalini Tommaso
(Fri Jan 17 2020 - 01:24:23 PST)
Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer
Stephan Schott
(Mon Jan 20 2020 - 07:01:36 PST)
Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer
Charles Lin
(Tue Jan 21 2020 - 06:30:36 PST)
[AMBER] vanilla Nose-Hoover thermostat availability
Sally Pias
(Thu Jan 16 2020 - 14:19:39 PST)
Re: [AMBER] vanilla Nose-Hoover thermostat availability
David Case
(Fri Jan 17 2020 - 06:43:07 PST)
Re: [AMBER] vanilla Nose-Hoover thermostat availability
Sally Pias
(Wed Jan 22 2020 - 17:41:00 PST)
[AMBER] pdb to mol2 conversion via antechamber
Sruthi Sudhakar
(Thu Jan 16 2020 - 22:54:51 PST)
Re: [AMBER] pdb to mol2 conversion via antechamber
Liao
(Fri Jan 17 2020 - 00:20:02 PST)
[AMBER] Workshop on Free Energy calculations in Muenster March 11-13 2020
Vlad Cojocaru
(Fri Jan 17 2020 - 01:32:27 PST)
[AMBER] RDF: corrupted trajectory
emanuele falbo
(Fri Jan 17 2020 - 08:02:09 PST)
Re: [AMBER] RDF: corrupted trajectory
Daniel Roe
(Fri Jan 17 2020 - 10:47:57 PST)
Re: [AMBER] RDF: corrupted trajectory
emanuele falbo
(Mon Jan 20 2020 - 02:24:06 PST)
Re: [AMBER] RDF: corrupted trajectory
Daniel Roe
(Tue Jan 21 2020 - 11:00:46 PST)
Re: [AMBER] RDF: corrupted trajectory
emanuele falbo
(Wed Jan 22 2020 - 01:40:51 PST)
[AMBER] Long syntax error on complex molecule
Manisha Yadav
(Fri Jan 17 2020 - 20:00:20 PST)
Re: [AMBER] Long syntax error on complex molecule
Thomas Cheatham
(Fri Jan 17 2020 - 20:11:19 PST)
[AMBER] Problem in Amber update
Kshatresh Dutta Dubey
(Sat Jan 18 2020 - 00:07:50 PST)
Re: [AMBER] Problem in Amber update
David Case
(Sat Jan 18 2020 - 05:27:10 PST)
Re: [AMBER] Problem in Amber update
Kshatresh Dutta Dubey
(Sun Jan 19 2020 - 05:14:27 PST)
[AMBER] GPU-AMBER18 installation on RTX2080Ti
ke.gohda.camm-kansai.org
(Sat Jan 18 2020 - 02:29:48 PST)
Re: [AMBER] GPU-AMBER18 installation on RTX2080Ti
Ross Walker
(Sat Jan 18 2020 - 11:32:13 PST)
Re: [AMBER] GPU-AMBER18 installation on RTX2080Ti
ke.gohda.camm-kansai.org
(Mon Jan 20 2020 - 03:30:38 PST)
[AMBER] rror: an illegal memory access was encountered launching kernel kNLSkinTest
Sruthi Sudhakar
(Sat Jan 18 2020 - 04:30:58 PST)
[AMBER] MMPBSA run failure
Billiot, Eugene
(Sat Jan 18 2020 - 04:45:31 PST)
Re: [AMBER] rror: an illegal memory access was encountered launching kernel kNLSkinTest
David Case
(Sat Jan 18 2020 - 05:31:36 PST)
[AMBER] defining a progress variable to be the z-component of some atom or group of atoms?
David Case
(Sat Jan 18 2020 - 05:14:29 PST)
Re: [AMBER] defining a progress variable to be the z-component of some atom or group of atoms?
Goetz, Andreas
(Sat Jan 18 2020 - 18:01:59 PST)
Re: [AMBER] defining a progress variable to be the z-component of some atom or group of atoms?
Gerardo Zerbetto De Palma
(Sat Jan 18 2020 - 18:26:19 PST)
Re: [AMBER] defining a progress variable to be the z-component of some atom or group of atoms?
Feng Pan
(Sun Jan 19 2020 - 08:31:08 PST)
Re: [AMBER] defining a progress variable to be the z-component of some atom or group of atoms?
Stephan Schott
(Mon Jan 20 2020 - 07:12:55 PST)
[AMBER] Problem regarding umbrella sampling
roomno sixtysix
(Sun Jan 19 2020 - 06:45:41 PST)
[AMBER] Problem regarding umbrella sampling
Rituparna Roy
(Sun Jan 19 2020 - 20:31:13 PST)
Re: [AMBER] Problem regarding umbrella sampling
David Case
(Mon Jan 20 2020 - 05:44:45 PST)
[AMBER] About ions coordinated to Zinc
MENDOZA Cesar
(Mon Jan 20 2020 - 06:45:22 PST)
Re: [AMBER] About ions coordinated to Zinc
MENDOZA Cesar
(Thu Jan 23 2020 - 07:23:05 PST)
Re: [AMBER] About ions coordinated to Zinc
MENDOZA Cesar
(Fri Jan 24 2020 - 15:18:38 PST)
[AMBER] sqm calculation with external charges not working
Anthony Bogetti
(Mon Jan 20 2020 - 07:53:08 PST)
Re: [AMBER] sqm calculation with external charges not working
Goetz, Andreas
(Tue Jan 21 2020 - 21:58:43 PST)
[AMBER] convergence of Ref energies in cpHMD
Kolattukudy P. Santo
(Mon Jan 20 2020 - 10:43:20 PST)
Re: [AMBER] convergence of Ref energies in cpHMD
Cruzeiro,Vinicius Wilian D
(Mon Jan 20 2020 - 12:15:54 PST)
Re: [AMBER] convergence of Ref energies in cpHMD
Kolattukudy P. Santo
(Mon Jan 20 2020 - 12:41:18 PST)
Re: [AMBER] convergence of Ref energies in cpHMD
Cruzeiro,Vinicius Wilian D
(Mon Jan 20 2020 - 14:27:11 PST)
Re: [AMBER] convergence of Ref energies in cpHMD
Kolattukudy P. Santo
(Tue Jan 21 2020 - 06:13:47 PST)
Re: [AMBER] convergence of Ref energies in cpHMD
Cruzeiro,Vinicius Wilian D
(Tue Jan 21 2020 - 23:43:35 PST)
Re: [AMBER] convergence of Ref energies in cpHMD
Kolattukudy P. Santo
(Wed Jan 22 2020 - 06:37:44 PST)
Re: [AMBER] convergence of Ref energies in cpHMD
Cruzeiro,Vinicius Wilian D
(Thu Jan 23 2020 - 14:38:23 PST)
[AMBER] Is there any sense in even trying to model large conformational dynamics with molecular dynamics?
Homeo Morphism
(Mon Jan 20 2020 - 11:15:52 PST)
Re: [AMBER] Is there any sense in even trying to model large conformational dynamics with molecular dynamics?
Gerardo Zerbetto De Palma
(Mon Jan 20 2020 - 11:24:30 PST)
Re: [AMBER] Is there any sense in even trying to model large conformational dynamics with molecular dynamics?
Carlos Simmerling
(Mon Jan 20 2020 - 11:59:07 PST)
[AMBER] NEB Simulations in Amber
SHAUNAK BADANI
(Mon Jan 20 2020 - 12:25:26 PST)
Re: [AMBER] NEB Simulations in Amber
Carlos Simmerling
(Mon Jan 20 2020 - 13:55:31 PST)
[AMBER] DUMPAVE digits
Santiago Movilla
(Mon Jan 20 2020 - 14:29:33 PST)
[AMBER] Reg. working of Periodic Boundary Conditions
DHEERAJ CHITARA
(Tue Jan 21 2020 - 06:25:23 PST)
Re: [AMBER] Reg. working of Periodic Boundary Conditions
David Case
(Tue Jan 21 2020 - 09:38:10 PST)
[AMBER] cpptraj_clucster
Lod King
(Tue Jan 21 2020 - 19:16:44 PST)
Re: [AMBER] cpptraj_clucster
Thayer, Kelly
(Wed Jan 29 2020 - 07:13:49 PST)
[AMBER] generating g-quadruplex DNA structures from a sequence
Vaibhav Dixit
(Tue Jan 21 2020 - 22:51:39 PST)
Re: [AMBER] generating g-quadruplex DNA structures from a sequence
David Case
(Wed Jan 22 2020 - 05:05:18 PST)
Re: [AMBER] generating g-quadruplex DNA structures from a sequence
Vaibhav Dixit
(Wed Jan 22 2020 - 21:09:14 PST)
Re: [AMBER] generating g-quadruplex DNA structures from a sequence
Satyaseelan C
(Thu Jan 23 2020 - 00:53:24 PST)
[AMBER] Wanting to get synchronized trajectory files
Abdullah Bin Faheem
(Wed Jan 22 2020 - 02:53:50 PST)
Re: [AMBER] Wanting to get synchronized trajectory files
David Case
(Wed Jan 22 2020 - 05:09:18 PST)
Re: [AMBER] Wanting to get synchronized trajectory files
Abdullah Bin Faheem
(Wed Jan 22 2020 - 07:05:28 PST)
Re: [AMBER] Wanting to get synchronized trajectory files
Carlos Simmerling
(Wed Jan 22 2020 - 07:43:43 PST)
Re: [AMBER] Wanting to get synchronized trajectory files
Abdullah Bin Faheem
(Wed Jan 22 2020 - 08:06:01 PST)
Re: [AMBER] Wanting to get synchronized trajectory files
Carlos Simmerling
(Wed Jan 22 2020 - 09:10:16 PST)
Re: [AMBER] Wanting to get synchronized trajectory files
Abdullah Bin Faheem
(Wed Jan 22 2020 - 10:58:14 PST)
Re: [AMBER] Wanting to get synchronized trajectory files
Gustaf Olsson
(Wed Jan 22 2020 - 05:47:36 PST)
[AMBER] Multiple GPU imstallation of AMBER 18 error
Sruthi Sudhakar
(Wed Jan 22 2020 - 22:54:08 PST)
Re: [AMBER] Multiple GPU imstallation of AMBER 18 error
Elvis Martis
(Thu Jan 23 2020 - 00:06:36 PST)
Re: [AMBER] Multiple GPU imstallation of AMBER 18 error
Sruthi Sudhakar
(Thu Jan 23 2020 - 00:17:11 PST)
Re: [AMBER] Multiple GPU imstallation of AMBER 18 error
Elvis Martis
(Thu Jan 23 2020 - 01:33:20 PST)
Re: [AMBER] Multiple GPU imstallation of AMBER 18 error
Sruthi Sudhakar
(Thu Jan 23 2020 - 02:08:46 PST)
Re: [AMBER] Multiple GPU imstallation of AMBER 18 error
Sruthi Sudhakar
(Thu Jan 23 2020 - 02:10:05 PST)
Re: [AMBER] Multiple GPU imstallation of AMBER 18 error
Sruthi Sudhakar
(Thu Jan 23 2020 - 03:39:54 PST)
Re: [AMBER] Multiple GPU imstallation of AMBER 18 error
Elvis Martis
(Thu Jan 23 2020 - 05:15:11 PST)
Re: [AMBER] Multiple GPU imstallation of AMBER 18 error
David Case
(Thu Jan 23 2020 - 06:39:31 PST)
Re: [AMBER] Multiple GPU imstallation of AMBER 18 error
Sruthi Sudhakar
(Thu Jan 23 2020 - 07:24:01 PST)
Re: [AMBER] Multiple GPU imstallation of AMBER 18 error
Elvis Martis
(Thu Jan 23 2020 - 07:38:03 PST)
Re: [AMBER] Multiple GPU imstallation of AMBER 18 error
Sruthi Sudhakar
(Thu Jan 23 2020 - 07:53:41 PST)
Re: [AMBER] Multiple GPU imstallation of AMBER 18 error
Sruthi Sudhakar
(Fri Jan 24 2020 - 02:13:20 PST)
Re: [AMBER] Multiple GPU imstallation of AMBER 18 error
Elvis Martis
(Fri Jan 24 2020 - 03:51:15 PST)
Re: [AMBER] Multiple GPU imstallation of AMBER 18 error
Sruthi Sudhakar
(Fri Jan 24 2020 - 20:48:14 PST)
Re: [AMBER] Multiple GPU imstallation of AMBER 18 error
Sruthi Sudhakar
(Fri Jan 24 2020 - 22:25:09 PST)
Re: [AMBER] Multiple GPU imstallation of AMBER 18 error
Elvis Martis
(Sat Jan 25 2020 - 18:45:45 PST)
[AMBER] Normal mode analysis using trajectory files
Divya Rai
(Wed Jan 22 2020 - 22:26:31 PST)
Re: [AMBER] Normal mode analysis using trajectory files
Elvis Martis
(Thu Jan 23 2020 - 00:08:52 PST)
[AMBER] Parameter Files for Nanopore made of Si3N4(Silicon Nitride)
Vishal Reddy
(Thu Jan 23 2020 - 02:05:25 PST)
[AMBER] Does anyone here use a99SB-disp force field and how did you obtain it?
Homeo Morphism
(Thu Jan 23 2020 - 02:44:52 PST)
Re: [AMBER] Does anyone here use a99SB-disp force field and how did you obtain it?
Anthony Cruz-Balberdy
(Thu Jan 23 2020 - 04:56:36 PST)
Re: [AMBER] Does anyone here use a99SB-disp force field and how did you obtain it?
Casalini Tommaso
(Thu Jan 23 2020 - 07:05:43 PST)
[AMBER] steered MD question
Baker, Joseph
(Thu Jan 23 2020 - 12:10:50 PST)
[AMBER] Shaw DE RNA ff in Amber format
amirhossein taghavi
(Thu Jan 23 2020 - 13:59:17 PST)
[AMBER] Autoimage problem
Agata Sowińska I34
(Fri Jan 24 2020 - 08:41:14 PST)
[AMBER] pmemd.cuda.MPI run error
Sruthi Sudhakar
(Mon Jan 27 2020 - 04:21:04 PST)
Re: [AMBER] pmemd.cuda.MPI run error
Gerardo Zerbetto De Palma
(Mon Jan 27 2020 - 03:52:05 PST)
Re: [AMBER] pmemd.cuda.MPI run error
Elvis Martis
(Mon Jan 27 2020 - 03:58:28 PST)
Re: [AMBER] pmemd.cuda.MPI run error
Sruthi Sudhakar
(Mon Jan 27 2020 - 04:49:12 PST)
Re: [AMBER] pmemd.cuda.MPI run error
Sruthi Sudhakar
(Mon Jan 27 2020 - 04:55:00 PST)
Re: [AMBER] pmemd.cuda.MPI run error
Gerardo Zerbetto De Palma
(Mon Jan 27 2020 - 04:31:08 PST)
Re: [AMBER] pmemd.cuda.MPI run error
Sruthi Sudhakar
(Mon Jan 27 2020 - 05:11:08 PST)
[AMBER] Fwd: CalcError: /truba/sw/centos6.4/app/amber/amber14/bin/sander failed with prmtop gas.complex.prmtop!
Rana Rehan Khalid
(Mon Jan 27 2020 - 08:51:02 PST)
[AMBER] About ferrocene
MENDOZA Cesar
(Mon Jan 27 2020 - 08:54:45 PST)
[AMBER] Calculation of mask for TI input
Airy Sanjeev
(Mon Jan 27 2020 - 20:22:34 PST)
Re: [AMBER] Calculation of mask for TI input
Carlos Simmerling
(Tue Jan 28 2020 - 02:40:09 PST)
[AMBER] Several alpha-helices stitched together - how would you stress-test it with MD?
Homeo Morphism
(Tue Jan 28 2020 - 02:48:35 PST)
Re: [AMBER] Several alpha-helices stitched together - how would you stress-test it with MD?
Carlos Simmerling
(Tue Jan 28 2020 - 02:52:49 PST)
[AMBER] Amber on windows 10
Nicolas Feldman
(Tue Jan 28 2020 - 04:14:39 PST)
Re: [AMBER] Amber on windows 10
Elvis Martis
(Tue Jan 28 2020 - 04:19:42 PST)
Re: [AMBER] Amber on windows 10
Nicolas Feldman
(Tue Jan 28 2020 - 04:33:33 PST)
Re: [AMBER] Amber on windows 10
Gustaf Olsson
(Tue Jan 28 2020 - 04:22:32 PST)
Re: [AMBER] Amber on windows 10
Nicolas Feldman
(Tue Jan 28 2020 - 04:27:06 PST)
Re: [AMBER] Amber on windows 10
Gustaf Olsson
(Tue Jan 28 2020 - 05:21:47 PST)
Re: [AMBER] Amber on windows 10
Gustaf Olsson
(Tue Jan 28 2020 - 07:08:14 PST)
Re: [AMBER] Amber on windows 10
Nicolas Feldman
(Tue Jan 28 2020 - 07:13:37 PST)
Re: [AMBER] Amber on windows 10
Elvis Martis
(Tue Jan 28 2020 - 07:22:22 PST)
[AMBER] About utilities to convert Amber input files for MD into the Tinker, NAMD, Genesis, or Desmond input files
Vlad
(Tue Jan 28 2020 - 20:00:19 PST)
Re: [AMBER] About utilities to convert Amber input files for MD into the Tinker, NAMD, Genesis, or Desmond input files
Elvis Martis
(Tue Jan 28 2020 - 20:17:49 PST)
[AMBER] kindly guide me
ALAMGIR KHAN
(Tue Jan 28 2020 - 21:00:54 PST)
Re: [AMBER] kindly guide me
Gustaf Olsson
(Tue Jan 28 2020 - 22:42:49 PST)
Re: [AMBER] kindly guide me
ALAMGIR KHAN
(Wed Jan 29 2020 - 01:43:08 PST)
[AMBER] gnuplot
MYRIAN TORRES RICO
(Wed Jan 29 2020 - 02:17:48 PST)
[AMBER] gnuplot
MYRIAN TORRES RICO
(Wed Jan 29 2020 - 02:18:56 PST)
[AMBER] sulfonamide parameters for correct geometry
Annachiara TINIVELLA
(Wed Jan 29 2020 - 04:31:25 PST)
[AMBER] how does one reply to a thread in a mailing list
Homeo Morphism
(Wed Jan 29 2020 - 07:26:57 PST)
Re: [AMBER] how does one reply to a thread in a mailing list
David Case
(Wed Jan 29 2020 - 11:08:18 PST)
[AMBER] Help building a model of a 2F-2S protein with MDPB.py
Gustavo Seabra
(Wed Jan 29 2020 - 10:57:18 PST)
Re: [AMBER] Help building a model of a 2F-2S protein with MDPB.py
MENDOZA Cesar
(Wed Jan 29 2020 - 12:25:47 PST)
Re: [AMBER] Help building a model of a 2F-2S protein with MDPB.py
MENDOZA Cesar
(Wed Jan 29 2020 - 12:27:36 PST)
[AMBER] Error in installing parallel version of AMBER18
dilrajl.bii.a-star.edu.sg
(Thu Jan 30 2020 - 06:51:57 PST)
Re: [AMBER] Error in installing parallel version of AMBER18
Scott Brozell
(Thu Jan 30 2020 - 11:55:53 PST)
[AMBER] postdoc DNA/RNA simulations
Jiri Sponer
(Thu Jan 30 2020 - 09:36:31 PST)
Re: [AMBER] postdoc DNA/RNA simulations
Nicolas Feldman
(Thu Jan 30 2020 - 10:14:06 PST)
[AMBER] usefrcascoords calculations
Lambach, Lauren
(Thu Jan 30 2020 - 14:25:28 PST)
[AMBER] Doubt regarding Collision frequency during NEB simulations
SHAUNAK BADANI
(Fri Jan 31 2020 - 11:37:03 PST)
Last message date
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Fri Jan 31 2020 - 12:00:02 PST
Archived on
: Wed Dec 25 2024 - 05:55:55 PST
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