Amber Archive Oct 2014 by thread
456 messages
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Starting
Tue Sep 30 2014 - 16:30:02 PDT,
Ending
Fri Oct 31 2014 - 14:00:02 PDT
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Re: [AMBER] writing trr trajectory
newamber list
(Tue Sep 30 2014 - 16:16:50 PDT)
Re: [AMBER] writing trr trajectory
Daniel Roe
(Wed Oct 01 2014 - 07:11:50 PDT)
Re: [AMBER] key word to pull out eigenvalues
newamber list
(Tue Sep 30 2014 - 16:30:11 PDT)
[AMBER] LIE FUNCTION
Loïc Etheve
(Wed Oct 01 2014 - 02:21:48 PDT)
Re: [AMBER] LIE FUNCTION
Jason Swails
(Wed Oct 01 2014 - 04:20:17 PDT)
Re: [AMBER] LIE FUNCTION
Jason Swails
(Wed Oct 01 2014 - 08:17:30 PDT)
[AMBER] switch from digest
amirhossein taghavi
(Wed Oct 01 2014 - 23:55:45 PDT)
Re: [AMBER] switch from digest
Jason Swails
(Thu Oct 02 2014 - 19:49:40 PDT)
[AMBER] RAM error during multiple MMGBSA runs
James Starlight
(Thu Oct 02 2014 - 00:36:05 PDT)
Re: [AMBER] RAM error during multiple MMGBSA runs
Ray Luo, Ph.D.
(Thu Oct 02 2014 - 13:24:05 PDT)
Re: [AMBER] RAM error during multiple MMGBSA runs
James Starlight
(Fri Oct 03 2014 - 01:45:17 PDT)
[AMBER] help: MD on DNA
pradeep pant
(Thu Oct 02 2014 - 03:33:58 PDT)
Re: [AMBER] help: MD on DNA
David A Case
(Thu Oct 02 2014 - 05:17:00 PDT)
[AMBER] help: MD on DNA
pradeep pant
(Fri Oct 03 2014 - 07:15:58 PDT)
Re: [AMBER] help: MD on DNA
Jason Swails
(Fri Oct 03 2014 - 09:23:37 PDT)
[AMBER] Problems with MMPBSA.py.MPI
James Starlight
(Fri Oct 03 2014 - 00:30:23 PDT)
[AMBER] carbon and nitrogen chemical shift restraints
Alexandra Balaceanu
(Fri Oct 03 2014 - 01:54:45 PDT)
Re: [AMBER] carbon and nitrogen chemical shift restraints
David A Case
(Fri Oct 03 2014 - 06:32:15 PDT)
Re: [AMBER] carbon and nitrogen chemical shift restraints
Alexandra Balaceanu
(Fri Oct 03 2014 - 12:03:59 PDT)
[AMBER] Cluster RMSD
Soumendranath Bhakat
(Fri Oct 03 2014 - 02:48:54 PDT)
Re: [AMBER] Cluster RMSD
Daniel Roe
(Fri Oct 03 2014 - 07:15:58 PDT)
[AMBER] Processing of the trajectories using ptraj
James Starlight
(Fri Oct 03 2014 - 05:13:18 PDT)
Re: [AMBER] Processing of the trajectories using ptraj
Daniel Roe
(Fri Oct 03 2014 - 07:09:22 PDT)
Re: [AMBER] Processing of the trajectories using ptraj
James Starlight
(Mon Oct 06 2014 - 00:15:41 PDT)
Re: [AMBER] Processing of the trajectories using ptraj
Daniel Roe
(Mon Oct 06 2014 - 07:59:34 PDT)
[AMBER] QM/MM in amber, PME when qm_theory='extern'
Aixiao Li
(Fri Oct 03 2014 - 06:57:28 PDT)
Re: [AMBER] QM/MM in amber, PME when qm_theory='extern'
Brian Radak
(Mon Oct 06 2014 - 14:27:59 PDT)
Re: [AMBER] QM/MM in amber, PME when qm_theory='extern'
Andreas Goetz
(Tue Oct 14 2014 - 22:00:19 PDT)
[AMBER] cpptraj Tutorial C1
George Tzotzos
(Fri Oct 03 2014 - 11:25:11 PDT)
Re: [AMBER] cpptraj Tutorial C1
George Tzotzos
(Fri Oct 03 2014 - 11:36:40 PDT)
Re: [AMBER] cpptraj Tutorial C1
Jason Swails
(Fri Oct 03 2014 - 11:50:06 PDT)
Re: [AMBER] cpptraj Tutorial C1
Daniel Roe
(Fri Oct 03 2014 - 11:57:56 PDT)
[AMBER] Tethering water molecules in the receptor
George Tzotzos
(Sat Oct 04 2014 - 12:37:01 PDT)
Re: [AMBER] Tethering water molecules in the receptor
Jason Swails
(Sat Oct 04 2014 - 14:09:00 PDT)
Re: [AMBER] Tethering water molecules in the receptor
George Tzotzos
(Sat Oct 04 2014 - 16:14:06 PDT)
Re: [AMBER] Tethering water molecules in the receptor
Jason Swails
(Sat Oct 04 2014 - 20:50:54 PDT)
[AMBER] Langevin thermostat in vacuu simulation o ..High RMSF of TEMP
CHAMI F.
(Sun Oct 05 2014 - 10:21:34 PDT)
Re: [AMBER] Langevin thermostat in vacuu simulation o ..High RMSF of TEMP
Jason Swails
(Sun Oct 05 2014 - 19:24:56 PDT)
[AMBER] Dummy atom and PMEMD
Miroslav Krepl
(Sun Oct 05 2014 - 13:11:58 PDT)
Re: [AMBER] Dummy atom and PMEMD
Jason Swails
(Sun Oct 05 2014 - 18:02:01 PDT)
Re: [AMBER] Dummy atom and PMEMD
Miroslav Krepl
(Mon Oct 06 2014 - 01:13:10 PDT)
Re: [AMBER] Dummy atom and PMEMD
Jason Swails
(Mon Oct 06 2014 - 04:26:38 PDT)
[AMBER] Trouble making frcmod file (ultimately to create prmtop file)
Evans, Shalton
(Mon Oct 06 2014 - 13:34:12 PDT)
Re: [AMBER] Trouble making frcmod file (ultimately to create prmtop file)
Jason Swails
(Mon Oct 06 2014 - 13:42:53 PDT)
Re: [AMBER] Trouble making frcmod file (ultimately to create prmtop file)
Brian Radak
(Mon Oct 06 2014 - 14:35:01 PDT)
[AMBER] On the enthropy estimation in MMPBSA
James Starlight
(Tue Oct 07 2014 - 00:39:51 PDT)
Re: [AMBER] On the enthropy estimation in MMPBSA
James Starlight
(Wed Oct 08 2014 - 01:30:55 PDT)
[AMBER] Chloroform box
Neha Gandhi
(Tue Oct 07 2014 - 00:49:12 PDT)
Re: [AMBER] Chloroform box
David A Case
(Tue Oct 07 2014 - 04:30:20 PDT)
Re: [AMBER] Chloroform box
Jason Swails
(Tue Oct 07 2014 - 04:52:18 PDT)
[AMBER] Need help for retrained MD
Sudhanshu Shanker
(Tue Oct 07 2014 - 03:37:59 PDT)
Re: [AMBER] Need help for retrained MD
Jason Swails
(Tue Oct 07 2014 - 04:55:58 PDT)
Re: [AMBER] Need help for retrained MD
Daniel Roe
(Tue Oct 07 2014 - 07:36:41 PDT)
[AMBER] Fwd: parallel amber installation failed
Fabian
(Tue Oct 07 2014 - 06:45:39 PDT)
Re: [AMBER] Fwd: parallel amber installation failed
Daniel Roe
(Tue Oct 07 2014 - 07:29:17 PDT)
Re: [AMBER] Fwd: parallel amber installation failed
Fabian Glaser
(Tue Oct 07 2014 - 09:42:58 PDT)
Re: [AMBER] Fwd: parallel amber installation failed
David A Case
(Tue Oct 07 2014 - 10:53:30 PDT)
Re: [AMBER] Fwd: parallel amber installation failed
Jason Swails
(Tue Oct 07 2014 - 10:58:59 PDT)
Re: [AMBER] Fwd: parallel amber installation failed
Fabian Gmail
(Tue Oct 07 2014 - 11:14:39 PDT)
Re: [AMBER] Fwd: parallel amber installation failed
Jason Swails
(Tue Oct 07 2014 - 10:55:49 PDT)
[AMBER] amber12 Installation Error MAC OS X
BERGY
(Tue Oct 07 2014 - 12:14:34 PDT)
Re: [AMBER] amber12 Installation Error MAC OS X
David A Case
(Tue Oct 07 2014 - 13:27:14 PDT)
Re: [AMBER] amber12 Installation Error MAC OS X
BERGY
(Tue Oct 07 2014 - 14:46:12 PDT)
Re: [AMBER] amber12 Installation Error MAC OS X
BERGY
(Tue Oct 07 2014 - 15:12:11 PDT)
[AMBER] RNA with Malachite Green simulation
Kasprzak, Wojciech (NIH/NCI) [C]
(Tue Oct 07 2014 - 13:15:31 PDT)
[AMBER] Lambda Exchange
Jeff Wereszczynski
(Tue Oct 07 2014 - 19:19:29 PDT)
Re: [AMBER] Lambda Exchange
Jason Swails
(Wed Oct 08 2014 - 05:18:38 PDT)
Re: [AMBER] Lambda Exchange
Jeff Wereszczynski
(Wed Oct 08 2014 - 10:23:22 PDT)
Re: [AMBER] Lambda Exchange
Jason Swails
(Wed Oct 08 2014 - 11:30:40 PDT)
Re: [AMBER] Lambda Exchange
Jeff Wereszczynski
(Wed Oct 08 2014 - 11:50:31 PDT)
Re: [AMBER] Lambda Exchange
Jason Swails
(Wed Oct 08 2014 - 12:29:53 PDT)
[AMBER] No AMBERHOME/dat/mtkpp folder
mmaestre.gate.sinica.edu.tw
(Tue Oct 07 2014 - 20:15:54 PDT)
Re: [AMBER] No AMBERHOME/dat/mtkpp folder
Jason Swails
(Wed Oct 08 2014 - 04:56:03 PDT)
Re: [AMBER] No AMBERHOME/dat/mtkpp folder
David A Case
(Wed Oct 08 2014 - 05:03:26 PDT)
Re: [AMBER] No AMBERHOME/dat/mtkpp folder
mmaestre.gate.sinica.edu.tw
(Wed Oct 08 2014 - 16:35:44 PDT)
Re: [AMBER] No AMBERHOME/dat/mtkpp folder
Jason Swails
(Wed Oct 08 2014 - 16:56:08 PDT)
[AMBER] Regarding dihedrals in GAFF need clarification
Arun Srikanth
(Wed Oct 08 2014 - 07:09:37 PDT)
Re: [AMBER] Regarding dihedrals in GAFF need clarification
Jason Swails
(Wed Oct 08 2014 - 07:19:58 PDT)
Re: [AMBER] Regarding dihedrals in GAFF need clarification
Arun Srikanth
(Wed Oct 08 2014 - 07:32:45 PDT)
Re: [AMBER] Regarding dihedrals in GAFF need clarification
Jason Swails
(Wed Oct 08 2014 - 07:35:22 PDT)
[AMBER] problems with "Could not find vdW"
Investigador Química
(Wed Oct 08 2014 - 07:40:50 PDT)
Re: [AMBER] problems with "Could not find vdW"
Jason Swails
(Wed Oct 08 2014 - 07:51:00 PDT)
Re: [AMBER] problems with "Could not find vdW"
Investigador Química
(Wed Oct 08 2014 - 08:07:36 PDT)
Re: [AMBER] problems with "Could not find vdW"
Jason Swails
(Wed Oct 08 2014 - 08:13:59 PDT)
Re: [AMBER] problems with "Could not find vdW"
Daniel Roe
(Wed Oct 08 2014 - 08:15:45 PDT)
Re: [AMBER] problems with "Could not find vdW"
Investigador Química
(Thu Oct 09 2014 - 06:59:17 PDT)
Re: [AMBER] problems with "Could not find vdW"
Daniel Roe
(Thu Oct 09 2014 - 07:08:02 PDT)
Re: [AMBER] problems with "Could not find vdW"
Investigador Química
(Thu Oct 09 2014 - 07:18:20 PDT)
[AMBER] Is there a way to maintain pdb coordinates into leap?
Jonathan Gough
(Wed Oct 08 2014 - 11:14:22 PDT)
Re: [AMBER] Is there a way to maintain pdb coordinates into leap?
Bill Ross
(Wed Oct 08 2014 - 11:48:12 PDT)
Re: [AMBER] Is there a way to maintain pdb coordinates into leap?
David A Case
(Wed Oct 08 2014 - 14:19:56 PDT)
Re: [AMBER] Is there a way to maintain pdb coordinates into leap?
Jonathan Gough
(Wed Oct 08 2014 - 18:10:21 PDT)
[AMBER] Problem on generating topology file of lithium based electrolyte using GAFF
Debashis Kundu
(Wed Oct 08 2014 - 16:56:47 PDT)
[AMBER] Torsion Scan
Zachary Davis
(Wed Oct 08 2014 - 20:31:24 PDT)
Re: [AMBER] Torsion Scan
Dwight McGee
(Wed Oct 08 2014 - 23:24:11 PDT)
[AMBER] Error: FFTW configure returned 77 during AMBER 12 installation
sunita.tifrh.res.in
(Thu Oct 09 2014 - 00:11:14 PDT)
Re: [AMBER] Error: FFTW configure returned 77 during AMBER 12 installation
Jason Swails
(Thu Oct 09 2014 - 05:30:53 PDT)
Re: [AMBER] Error: FFTW configure returned 77 during AMBER 12 installation
sunita.tifrh.res.in
(Thu Oct 09 2014 - 06:02:20 PDT)
[AMBER] Zinc Paramitarization
Patrick Appiah-Kubi
(Thu Oct 09 2014 - 01:02:28 PDT)
Re: [AMBER] Zinc Paramitarization
Pengfei Li
(Thu Oct 09 2014 - 08:25:50 PDT)
[AMBER] atom coordinate disagreement with sander TI
Hannes Loeffler
(Thu Oct 09 2014 - 04:15:27 PDT)
Re: [AMBER] atom coordinate disagreement with sander TI
David A Case
(Thu Oct 09 2014 - 05:25:52 PDT)
Re: [AMBER] atom coordinate disagreement with sander TI
Hannes Loeffler
(Thu Oct 09 2014 - 08:15:30 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Pablo Ródenas
(Thu Oct 09 2014 - 07:22:37 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Scott Le Grand
(Thu Oct 09 2014 - 07:58:26 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Scott Le Grand
(Thu Oct 09 2014 - 08:06:14 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Scott Le Grand
(Thu Oct 09 2014 - 08:09:46 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Pablo Ródenas
(Thu Oct 09 2014 - 08:20:38 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Scott Le Grand
(Thu Oct 09 2014 - 08:23:37 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Scott Le Grand
(Thu Oct 09 2014 - 08:25:28 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Pablo Ródenas
(Thu Oct 09 2014 - 08:44:42 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Pablo Ródenas
(Thu Oct 09 2014 - 08:54:37 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Scott Le Grand
(Thu Oct 09 2014 - 09:06:43 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Pablo Ródenas
(Thu Oct 09 2014 - 23:36:43 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Scott Le Grand
(Fri Oct 10 2014 - 12:16:41 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Pablo Ródenas
(Sun Oct 12 2014 - 23:45:34 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Pablo Ródenas
(Tue Oct 14 2014 - 00:44:23 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Scott Le Grand
(Tue Oct 14 2014 - 06:54:15 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Pablo Ródenas
(Tue Oct 14 2014 - 07:03:02 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Scott Le Grand
(Tue Oct 14 2014 - 09:11:37 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Pablo Ródenas
(Tue Oct 28 2014 - 01:39:25 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
Scott Le Grand
(Thu Oct 09 2014 - 08:54:42 PDT)
[AMBER] Zinc Parameterization
Patrick Appiah-Kubi
(Thu Oct 09 2014 - 08:26:14 PDT)
[AMBER] cpptraj hbond: query on output
George Tzotzos
(Thu Oct 09 2014 - 13:33:25 PDT)
Re: [AMBER] cpptraj hbond: query on output
Daniel Roe
(Thu Oct 09 2014 - 15:24:35 PDT)
Re: [AMBER] cpptraj hbond: query on output
George Tzotzos
(Thu Oct 09 2014 - 17:00:58 PDT)
Re: [AMBER] cpptraj hbond: query on output
Daniel Roe
(Thu Oct 09 2014 - 18:14:53 PDT)
[AMBER] force field for lithium ion
Evans, Shalton
(Thu Oct 09 2014 - 16:11:11 PDT)
Re: [AMBER] force field for lithium ion
Mohd Farid Ismail
(Thu Oct 09 2014 - 16:38:58 PDT)
[AMBER] Questions about restarting REMD simulations
王漠野
(Thu Oct 09 2014 - 23:25:58 PDT)
Re: [AMBER] Questions about restarting REMD simulations
Daniel Roe
(Fri Oct 10 2014 - 06:48:16 PDT)
Re: [AMBER] Questions about restarting REMD simulations
王漠野
(Fri Oct 10 2014 - 19:01:00 PDT)
Re: [AMBER] Questions about restarting REMD simulations
Jason Swails
(Fri Oct 10 2014 - 12:41:17 PDT)
Re: [AMBER] Questions about restarting REMD simulations
王漠野
(Fri Oct 10 2014 - 18:54:26 PDT)
Re: [AMBER] Questions about restarting REMD simulations
Jason Swails
(Fri Oct 10 2014 - 19:01:49 PDT)
[AMBER] CUDA test failed
Niels Geudens
(Fri Oct 10 2014 - 03:42:56 PDT)
Re: [AMBER] CUDA test failed
Jason Swails
(Fri Oct 10 2014 - 09:25:21 PDT)
[AMBER] crashing multisander with TI/dummy
Hannes Loeffler
(Fri Oct 10 2014 - 04:11:21 PDT)
[AMBER] Restarting MD production run
Soumendranath Bhakat
(Sat Oct 11 2014 - 05:21:41 PDT)
Re: [AMBER] Restarting MD production run
Daniel Roe
(Sat Oct 11 2014 - 10:07:07 PDT)
[AMBER] Forcefield_PTM
Sourav Purohit
(Sat Oct 11 2014 - 11:22:12 PDT)
Re: [AMBER] Forcefield_PTM
Adrian Roitberg
(Sat Oct 11 2014 - 15:54:09 PDT)
Re: [AMBER] Forcefield_PTM
Ying-Chieh Sun
(Sun Oct 12 2014 - 20:04:21 PDT)
Re: [AMBER] Forcefield_PTM
Sourav Purohit
(Mon Oct 13 2014 - 02:35:31 PDT)
[AMBER] solvation free energy
kirtana S
(Sat Oct 11 2014 - 22:15:17 PDT)
Re: [AMBER] solvation free energy
David A Case
(Sun Oct 12 2014 - 05:38:04 PDT)
Re: [AMBER] solvation free energy
kirtana S
(Sun Oct 12 2014 - 12:58:06 PDT)
Re: [AMBER] solvation free energy
David A Case
(Sun Oct 12 2014 - 13:44:03 PDT)
[AMBER] Calcium possibly replaced by carbon with MCPB
mmaestre.gate.sinica.edu.tw
(Sun Oct 12 2014 - 17:00:12 PDT)
Re: [AMBER] Calcium possibly replaced by carbon with MCPB
Ken Merz
(Mon Oct 13 2014 - 05:06:03 PDT)
Re: [AMBER] Calcium possibly replaced by carbon with MCPB
mmaestre.gate.sinica.edu.tw
(Mon Oct 13 2014 - 07:22:03 PDT)
Re: [AMBER] Calcium possibly replaced by carbon with MCPB
Ken Merz
(Mon Oct 13 2014 - 07:39:03 PDT)
Re: [AMBER] Calcium possibly replaced by carbon with MCPB
Pengfei Li
(Mon Oct 13 2014 - 07:45:43 PDT)
Re: [AMBER] Calcium possibly replaced by carbon with MCPB
mmaestre.gate.sinica.edu.tw
(Mon Oct 13 2014 - 16:22:45 PDT)
Re: [AMBER] Calcium possibly replaced by carbon with MCPB
mmaestre.gate.sinica.edu.tw
(Mon Oct 13 2014 - 16:19:41 PDT)
Re: [AMBER] Calcium possibly replaced by carbon with MCPB
FyD
(Mon Oct 13 2014 - 12:40:29 PDT)
Re: [AMBER] Calcium possibly replaced by carbon with MCPB
mmaestre.gate.sinica.edu.tw
(Mon Oct 13 2014 - 16:28:38 PDT)
Re: [AMBER] Calcium possibly replaced by carbon with MCPB
Pengfei Li
(Tue Oct 14 2014 - 08:26:44 PDT)
Re: [AMBER] Calcium possibly replaced by carbon with MCPB
Pengfei Li
(Tue Oct 14 2014 - 08:30:12 PDT)
Re: [AMBER] Calcium possibly replaced by carbon with MCPB
mmaestre.gate.sinica.edu.tw
(Tue Oct 14 2014 - 15:11:34 PDT)
Re: [AMBER] Calcium possibly replaced by carbon with MCPB
mmaestre.gate.sinica.edu.tw
(Tue Oct 14 2014 - 18:25:07 PDT)
Re: [AMBER] Calcium possibly replaced by carbon with MCPB
Pengfei Li
(Tue Oct 14 2014 - 21:17:05 PDT)
Re: [AMBER] solvation free energy
kirtana S
(Mon Oct 13 2014 - 21:53:58 PDT)
Re: [AMBER] solvation free energy
kirtana S
(Mon Oct 13 2014 - 22:07:27 PDT)
Re: [AMBER] solvation free energy
David A Case
(Tue Oct 14 2014 - 05:27:23 PDT)
[AMBER] About error of the Pmemd.cuda (14)/ aMD
Yeng-Tseng Wang
(Sun Oct 12 2014 - 07:15:07 PDT)
Re: [AMBER] About error of the Pmemd.cuda (14)/ aMD
Daniel Roe
(Sun Oct 12 2014 - 09:34:59 PDT)
[AMBER] dendrimer-query
Martiniano Bello Ramirez
(Sun Oct 12 2014 - 09:59:42 PDT)
Re: [AMBER] dendrimer-query
Daniel Roe
(Sun Oct 12 2014 - 10:14:57 PDT)
Re: [AMBER] dendrimer-query
Vishal Maingi
(Mon Oct 13 2014 - 08:33:34 PDT)
Re: [AMBER] dendrimer-query
Daniel Roe
(Tue Oct 14 2014 - 13:49:24 PDT)
Re: [AMBER] dendrimer-query
Vishal Maingi
(Thu Oct 16 2014 - 08:03:09 PDT)
[AMBER] why total energy of the system is on the rise in NVE ensemble
zhangmk
(Sun Oct 12 2014 - 19:43:03 PDT)
Re: [AMBER] why total energy of the system is on the rise in NVE ensemble
James Maier
(Sun Oct 12 2014 - 19:52:58 PDT)
Re: [AMBER] why total energy of the system is on the rise in NVE ensemble
Hector A. Baldoni
(Tue Oct 14 2014 - 16:34:16 PDT)
Re: [AMBER] why total energy of the system is on the rise in NVE ensemble
David A Case
(Wed Oct 15 2014 - 05:58:12 PDT)
[AMBER] DFTB3 in Amber
Eric Lang
(Sun Oct 12 2014 - 20:26:02 PDT)
Re: [AMBER] DFTB3 in Amber
Gustavo Seabra
(Mon Oct 13 2014 - 05:50:07 PDT)
[AMBER] Setting exclusions correctly
Arun Srikanth
(Mon Oct 13 2014 - 00:12:15 PDT)
Re: [AMBER] Setting exclusions correctly
Jason Swails
(Tue Oct 14 2014 - 14:12:28 PDT)
Re: [AMBER] Setting exclusions correctly
Daniel Roe
(Tue Oct 14 2014 - 14:13:38 PDT)
Re: [AMBER] Setting exclusions correctly
Arun Srikanth
(Tue Oct 14 2014 - 15:38:33 PDT)
Re: [AMBER] Setting exclusions correctly
Jason Swails
(Wed Oct 15 2014 - 20:42:33 PDT)
[AMBER] Problem with lone pair
Giachetti Andrea - CERM
(Mon Oct 13 2014 - 01:23:03 PDT)
Re: [AMBER] Problem with lone pair
Jason Swails
(Tue Oct 14 2014 - 14:37:17 PDT)
[AMBER] Building Amber 14 for Intel PHIs
Baker D.J.
(Mon Oct 13 2014 - 02:10:31 PDT)
Re: [AMBER] Building Amber 14 for Intel PHIs
Ross Walker
(Mon Oct 13 2014 - 11:31:09 PDT)
Re: [AMBER] Building Amber 14 for Intel PHIs
Baker D.J.
(Tue Oct 14 2014 - 01:44:18 PDT)
[AMBER] Problem installing amber14
肖立
(Mon Oct 13 2014 - 11:08:44 PDT)
[AMBER] ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 46946 0
Hirdesh Kumar
(Mon Oct 13 2014 - 13:19:50 PDT)
Re: [AMBER] ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 46946 0
David A Case
(Mon Oct 13 2014 - 13:28:37 PDT)
Re: [AMBER] ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 46946 0
Hirdesh Kumar
(Mon Oct 13 2014 - 13:41:58 PDT)
Re: [AMBER] ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 46946 0
David A Case
(Mon Oct 13 2014 - 18:02:29 PDT)
[AMBER] How to install sander.MPI?
Zhong, Roger
(Mon Oct 13 2014 - 13:50:11 PDT)
Re: [AMBER] How to install sander.MPI?
David A Case
(Mon Oct 13 2014 - 18:05:55 PDT)
[AMBER] Amber 14 compile error
汪盛
(Mon Oct 13 2014 - 15:12:26 PDT)
Re: [AMBER] Amber 14 compile error
David A Case
(Mon Oct 13 2014 - 18:10:12 PDT)
[AMBER] principal axes cpptraj
Asmita Gupta
(Tue Oct 14 2014 - 04:25:59 PDT)
Re: [AMBER] principal axes cpptraj
Daniel Roe
(Tue Oct 14 2014 - 13:44:30 PDT)
[AMBER] Errors while attempting .prmtop file production
Evans, Shalton
(Tue Oct 14 2014 - 09:09:02 PDT)
Re: [AMBER] Errors while attempting .prmtop file production
David A Case
(Tue Oct 14 2014 - 12:12:15 PDT)
[AMBER] GIST dx files
Gard Nelson
(Tue Oct 14 2014 - 11:42:35 PDT)
Re: [AMBER] GIST dx files
Jonathan Gough
(Tue Oct 14 2014 - 12:34:28 PDT)
Re: [AMBER] GIST dx files
Nguyen, Crystal
(Tue Oct 14 2014 - 12:31:59 PDT)
Re: [AMBER] GIST dx files
Gard Nelson
(Tue Oct 14 2014 - 15:23:51 PDT)
[AMBER] Loss of secondary structure in GB simulations
Nihal Korkmaz
(Tue Oct 14 2014 - 13:50:13 PDT)
Re: [AMBER] Loss of secondary structure in GB simulations
Carlos Simmerling
(Tue Oct 14 2014 - 17:19:14 PDT)
Re: [AMBER] Loss of secondary structure in GB simulations
Nihal Korkmaz
(Tue Oct 14 2014 - 18:32:32 PDT)
Re: [AMBER] Loss of secondary structure in GB simulations
Hai Nguyen
(Tue Oct 14 2014 - 22:00:49 PDT)
Re: [AMBER] Loss of secondary structure in GB simulations
Nihal Korkmaz
(Wed Oct 15 2014 - 14:29:51 PDT)
Re: [AMBER] Loss of secondary structure in GB simulations
Nhai
(Wed Oct 15 2014 - 15:49:34 PDT)
[AMBER] Amber for beginner
Suraya Abdul Sani
(Tue Oct 14 2014 - 17:21:29 PDT)
Re: [AMBER] Amber for beginner
Jonathan Gough
(Tue Oct 14 2014 - 18:01:40 PDT)
Re: [AMBER] Amber for beginner
Raman Parkesh
(Tue Oct 14 2014 - 20:01:55 PDT)
[AMBER] How can I do MD simulation of a protein-ligand complex where the ligand is covalently attached to the protein
Bikash Ranjan Sahoo
(Tue Oct 14 2014 - 21:04:54 PDT)
[AMBER] How can I do MD simulation of a protein-ligand complex where the ligand is covalently attached to the protein
Bikash Ranjan Sahoo
(Wed Oct 15 2014 - 06:01:49 PDT)
[AMBER] TI and FEW
sabine.ruppel.boehringer-ingelheim.com
(Wed Oct 15 2014 - 13:11:22 PDT)
Re: [AMBER] TI and FEW
David A Case
(Wed Oct 15 2014 - 17:57:07 PDT)
Re: [AMBER] TI and FEW
sabine.ruppel.boehringer-ingelheim.com
(Thu Oct 16 2014 - 06:03:57 PDT)
Re: [AMBER] TI and FEW
David A Case
(Thu Oct 16 2014 - 06:32:42 PDT)
Re: [AMBER] TI and FEW
Nadine Homeyer
(Mon Oct 20 2014 - 06:38:12 PDT)
[AMBER] Setting exclusions - am i overcounting ?
Arun Srikanth
(Wed Oct 15 2014 - 14:56:12 PDT)
Re: [AMBER] Setting exclusions - am i overcounting ?
Daniel Roe
(Wed Oct 15 2014 - 15:57:55 PDT)
Re: [AMBER] Setting exclusions - am i overcounting ?
Arun Srikanth
(Wed Oct 15 2014 - 17:05:23 PDT)
Re: [AMBER] Setting exclusions - am i overcounting ?
Jason Swails
(Wed Oct 15 2014 - 17:51:12 PDT)
[AMBER] How can I do MD simulation of a protein-ligand complex where the ligand is covalently attached to the protein
Bikash Ranjan Sahoo
(Wed Oct 15 2014 - 17:50:03 PDT)
Re: [AMBER] Setting exclusions - am i overcounting ?-Last question
Arun Srikanth
(Wed Oct 15 2014 - 19:54:42 PDT)
Re: [AMBER] Setting exclusions - am i overcounting ?-Last question
Jason Swails
(Wed Oct 15 2014 - 21:24:38 PDT)
Re: [AMBER] Setting exclusions - am i overcounting ?-Last question
Arun Srikanth
(Wed Oct 15 2014 - 22:35:59 PDT)
[AMBER] Small NAB program: Not getting desired output
Himanshu Joshi
(Wed Oct 15 2014 - 22:41:28 PDT)
Re: [AMBER] Small NAB program: Not getting desired output
Himanshu Joshi
(Wed Oct 15 2014 - 23:23:00 PDT)
Re: [AMBER] Small NAB program: Not getting desired output
David A Case
(Thu Oct 16 2014 - 05:11:07 PDT)
Re: [AMBER] Small NAB program: Not getting desired output
Himanshu Joshi
(Fri Oct 17 2014 - 00:45:39 PDT)
Re: [AMBER] Small NAB program: Not getting desired output
David A Case
(Fri Oct 17 2014 - 05:30:41 PDT)
[AMBER] amber-Gaussian
王珍
(Thu Oct 16 2014 - 05:41:43 PDT)
[AMBER] Plotting Issue
Soumendranath Bhakat
(Thu Oct 16 2014 - 07:26:49 PDT)
Re: [AMBER] Plotting Issue
Jason Swails
(Thu Oct 16 2014 - 07:55:18 PDT)
[AMBER] Problem with input coordinates file
Francesco Gentile
(Thu Oct 16 2014 - 10:55:19 PDT)
Re: [AMBER] Problem with input coordinates file
Daniel Roe
(Thu Oct 16 2014 - 12:52:36 PDT)
Re: [AMBER] Problem with input coordinates file
Francesco Gentile
(Thu Oct 16 2014 - 14:06:54 PDT)
Re: [AMBER] Problem with input coordinates file
Daniel Roe
(Thu Oct 16 2014 - 14:36:01 PDT)
Re: [AMBER] Problem with input coordinates file
Daniel Roe
(Fri Oct 17 2014 - 12:23:17 PDT)
Re: [AMBER] Problem with input coordinates file
Francesco Gentile
(Fri Oct 17 2014 - 13:01:13 PDT)
Re: [AMBER] Problem with input coordinates file
Francesco Gentile
(Tue Oct 21 2014 - 13:05:00 PDT)
[AMBER] Loadpdb in Tleap takes forever
Ahmed Ayoub
(Thu Oct 16 2014 - 11:16:44 PDT)
Re: [AMBER] Loadpdb in Tleap takes forever
Daniel Roe
(Thu Oct 16 2014 - 12:55:26 PDT)
[AMBER] install error after updates
Nihal Korkmaz
(Thu Oct 16 2014 - 11:22:42 PDT)
Re: [AMBER] install error after updates
Daniel Roe
(Thu Oct 16 2014 - 12:24:57 PDT)
[AMBER] source leaprc.constph error
jinfeng liu
(Thu Oct 16 2014 - 15:07:24 PDT)
Re: [AMBER] source leaprc.constph error
Jason Swails
(Thu Oct 16 2014 - 16:11:24 PDT)
Re: [AMBER] source leaprc.constph error
jinfeng liu
(Thu Oct 16 2014 - 17:29:35 PDT)
Re: [AMBER] source leaprc.constph error
Jason Swails
(Thu Oct 16 2014 - 17:51:37 PDT)
Re: [AMBER] source leaprc.constph error
jinfeng liu
(Thu Oct 16 2014 - 18:12:49 PDT)
[AMBER] Which GPU is recommended?
xueqiaoup.gmail.com
(Thu Oct 16 2014 - 22:29:52 PDT)
Re: [AMBER] Which GPU is recommended?
Ross Walker
(Fri Oct 17 2014 - 12:16:04 PDT)
Re: [AMBER] Which GPU is recommended?
Alexander Metz
(Wed Oct 22 2014 - 03:54:31 PDT)
Re: [AMBER] Which GPU is recommended?
Jason Swails
(Wed Oct 22 2014 - 05:37:00 PDT)
Re: [AMBER] Need help for retrained MD (Daniel Roe)
Sudhanshu Shanker
(Fri Oct 17 2014 - 00:20:40 PDT)
Re: [AMBER] Need help for retrained MD (Daniel Roe)
Daniel Roe
(Fri Oct 17 2014 - 06:54:54 PDT)
[AMBER] Jarzynski SMD
George Tzotzos
(Fri Oct 17 2014 - 12:39:19 PDT)
Re: [AMBER] Jarzynski SMD
Jason Swails
(Fri Oct 17 2014 - 14:38:47 PDT)
[AMBER] thanks
zayan alhalabi
(Sat Oct 18 2014 - 07:45:10 PDT)
[AMBER] Regarding impropers from parmed.py and guessing from bond topology
Arun Srikanth
(Sat Oct 18 2014 - 14:38:36 PDT)
Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology
Daniel Roe
(Sat Oct 18 2014 - 16:24:23 PDT)
Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology
Arun Srikanth
(Sat Oct 18 2014 - 20:20:41 PDT)
Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology
Jason Swails
(Sat Oct 18 2014 - 21:52:51 PDT)
Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology
Arun Srikanth
(Sun Oct 19 2014 - 21:16:10 PDT)
Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology
Jason Swails
(Sun Oct 19 2014 - 21:27:52 PDT)
Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology
Arun Srikanth
(Sun Oct 19 2014 - 21:45:08 PDT)
Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology
Jason Swails
(Sun Oct 19 2014 - 23:08:30 PDT)
Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology
Arun Srikanth
(Sun Oct 19 2014 - 23:24:39 PDT)
Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology
Jason Swails
(Sat Oct 18 2014 - 16:27:12 PDT)
Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology
David A Case
(Sat Oct 18 2014 - 18:13:59 PDT)
[AMBER] solvation of a pdb file
Robin Jain
(Sun Oct 19 2014 - 08:19:37 PDT)
Re: [AMBER] solvation of a pdb file
David A Case
(Sun Oct 19 2014 - 10:47:46 PDT)
[AMBER] Fwd: Desmond trajectory use with AMBER
D.A. Ragland
(Sun Oct 19 2014 - 11:26:28 PDT)
Re: [AMBER] Fwd: Desmond trajectory use with AMBER
Daniel Roe
(Sun Oct 19 2014 - 11:49:37 PDT)
Re: [AMBER] Desmond trajectory use with AMBER
D.A. Ragland
(Sun Oct 19 2014 - 11:53:11 PDT)
Re: [AMBER] Desmond trajectory use with AMBER
Daniel Roe
(Sun Oct 19 2014 - 12:06:49 PDT)
Re: [AMBER] Desmond trajectory use with AMBER
D.A. Ragland
(Sun Oct 19 2014 - 12:09:36 PDT)
Re: [AMBER] Desmond trajectory use with AMBER
Daniel Roe
(Sun Oct 19 2014 - 12:20:01 PDT)
Re: [AMBER] Fwd: Desmond trajectory use with AMBER
jojartb.jgypk.u-szeged.hu
(Sun Oct 19 2014 - 21:15:39 PDT)
[AMBER] Heating Problem
jinfeng liu
(Sun Oct 19 2014 - 11:49:21 PDT)
Re: [AMBER] Heating Problem
Daniel Roe
(Sun Oct 19 2014 - 12:01:39 PDT)
[AMBER] Parameters for Boron atom
王璇
(Sun Oct 19 2014 - 18:26:39 PDT)
Re: [AMBER] Parameters for Boron atom
David A Case
(Mon Oct 20 2014 - 05:06:08 PDT)
[AMBER] Complex MD with protein ligand covalent bond
Bikash Ranjan Sahoo
(Mon Oct 20 2014 - 00:01:36 PDT)
Re: [AMBER] Complex MD with protein ligand covalent bond
David A Case
(Mon Oct 20 2014 - 05:10:28 PDT)
[AMBER] MMGBSA & igb 8
jojartb.jgypk.u-szeged.hu
(Mon Oct 20 2014 - 03:01:27 PDT)
Re: [AMBER] MMGBSA & igb 8
Jason Swails
(Mon Oct 20 2014 - 07:34:01 PDT)
Re: [AMBER] MMGBSA & igb 8
Carlos Simmerling
(Mon Oct 20 2014 - 07:43:06 PDT)
[AMBER] Problem regarding Chamber
Shubhadip Das
(Mon Oct 20 2014 - 04:28:43 PDT)
Re: [AMBER] Problem regarding Chamber
Jason Swails
(Mon Oct 20 2014 - 07:32:12 PDT)
Re: [AMBER] Problem regarding Chamber
Jason Swails
(Thu Oct 23 2014 - 00:45:33 PDT)
Re: [AMBER] Problem regarding Chamber
Jason Swails
(Fri Oct 24 2014 - 08:14:56 PDT)
[AMBER] Carboxyl and Carboxylate groups with GLYCAM
sa
(Mon Oct 20 2014 - 08:52:47 PDT)
Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM
Lachele Foley
(Tue Oct 21 2014 - 10:44:32 PDT)
Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM
sa
(Tue Oct 21 2014 - 11:33:36 PDT)
Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM
Lachele Foley
(Tue Oct 21 2014 - 13:06:12 PDT)
Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM
sa
(Tue Oct 21 2014 - 13:32:59 PDT)
Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM
Lachele Foley
(Tue Oct 21 2014 - 13:57:27 PDT)
Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM
sa
(Tue Oct 21 2014 - 14:24:21 PDT)
[AMBER] How can I get amber know calcium
jinfeng liu
(Mon Oct 20 2014 - 09:35:44 PDT)
Re: [AMBER] How can I get amber know calcium
Sajeewa Pemasinghe
(Mon Oct 20 2014 - 10:41:44 PDT)
Re: [AMBER] How can I get amber know calcium
Jason Swails
(Mon Oct 20 2014 - 10:44:23 PDT)
Re: [AMBER] How can I get amber know calcium
jinfeng liu
(Mon Oct 20 2014 - 10:57:29 PDT)
Re: [AMBER] How can I get amber know calcium
Chinthaka Ratnaweera
(Mon Oct 20 2014 - 11:28:01 PDT)
Re: [AMBER] How can I get amber know calcium
Pengfei Li
(Mon Oct 20 2014 - 11:38:20 PDT)
Re: [AMBER] How can I get amber know calcium
Chinthaka Ratnaweera
(Mon Oct 20 2014 - 11:47:19 PDT)
Re: [AMBER] How can I get amber know calcium
Pengfei Li
(Mon Oct 20 2014 - 11:50:18 PDT)
Re: [AMBER] How can I get amber know calcium
Ken Merz
(Mon Oct 20 2014 - 11:50:47 PDT)
Re: [AMBER] How can I get amber know calcium
Chinthaka Ratnaweera
(Mon Oct 20 2014 - 12:09:44 PDT)
Re: [AMBER] How can I get amber know calcium
Pengfei Li
(Mon Oct 20 2014 - 14:08:33 PDT)
Re: [AMBER] How can I get amber know calcium
mmaestre.gate.sinica.edu.tw
(Mon Oct 20 2014 - 16:15:09 PDT)
[AMBER] Chains missing during the simulation
Harshavardhan Khare
(Tue Oct 21 2014 - 00:56:58 PDT)
Re: [AMBER] Chains missing during the simulation
Jason Swails
(Tue Oct 21 2014 - 04:39:46 PDT)
Re: [AMBER] Chains missing during the simulation
Harshavardhan Khare
(Wed Oct 22 2014 - 04:23:31 PDT)
[AMBER] Forcefield_PTM
Sourav Purohit
(Tue Oct 21 2014 - 05:25:40 PDT)
Re: [AMBER] Forcefield_PTM
Jason Swails
(Tue Oct 21 2014 - 06:02:30 PDT)
Re: [AMBER] Forcefield_PTM
David A Case
(Tue Oct 21 2014 - 07:47:22 PDT)
Re: [AMBER] Forcefield_PTM
Sourav Purohit
(Tue Oct 21 2014 - 08:35:00 PDT)
[AMBER] Cpptraj: Move origin to specific coordinates
Waldner, Birgit
(Tue Oct 21 2014 - 06:09:31 PDT)
Re: [AMBER] Cpptraj: Move origin to specific coordinates
Daniel Roe
(Tue Oct 21 2014 - 08:06:58 PDT)
Re: [AMBER] Cpptraj: Move origin to specific coordinates
Waldner, Birgit
(Tue Oct 21 2014 - 08:37:15 PDT)
Re: [AMBER] Cpptraj: Move origin to specific coordinates
Daniel Roe
(Tue Oct 21 2014 - 09:07:31 PDT)
[AMBER] BSUB on LSF cluster
D.A. Ragland
(Tue Oct 21 2014 - 14:54:55 PDT)
Re: [AMBER] BSUB on LSF cluster
Jason Swails
(Tue Oct 21 2014 - 17:10:02 PDT)
Re: [AMBER] BSUB on LSF cluster
D.A. Ragland
(Tue Oct 21 2014 - 17:12:02 PDT)
Re: [AMBER] BSUB on LSF cluster
Jason Swails
(Tue Oct 21 2014 - 17:56:05 PDT)
Re: [AMBER] BSUB on LSF cluster
D.A. Ragland
(Tue Oct 21 2014 - 17:18:47 PDT)
[AMBER] Info About GPU and PMEMD versions
Lorenzo Gontrani
(Wed Oct 22 2014 - 01:55:50 PDT)
Re: [AMBER] Info About GPU and PMEMD versions
Jason Swails
(Wed Oct 22 2014 - 05:55:33 PDT)
Re: [AMBER] Info About GPU and PMEMD versions
Ross Walker
(Wed Oct 22 2014 - 07:56:30 PDT)
[AMBER] ANTECHAMBER tutorial
Sourav Purohit
(Wed Oct 22 2014 - 03:35:04 PDT)
Re: [AMBER] ANTECHAMBER tutorial
Jason Swails
(Wed Oct 22 2014 - 05:41:57 PDT)
Re: [AMBER] ANTECHAMBER tutorial
Sourav Purohit
(Wed Oct 22 2014 - 05:43:29 PDT)
[AMBER] Forcefield for RNA
Asfa Ali
(Wed Oct 22 2014 - 22:52:47 PDT)
Re: [AMBER] Forcefield for RNA
Jiri Sponer
(Thu Oct 23 2014 - 00:57:06 PDT)
Re: [AMBER] Forcefield for RNA
Jiri Sponer
(Thu Oct 23 2014 - 01:12:50 PDT)
Re: [AMBER] Forcefield for RNA
Ilyas Yildirim
(Thu Oct 23 2014 - 02:26:01 PDT)
Re: [AMBER] Forcefield for RNA
Jason Swails
(Thu Oct 23 2014 - 04:07:19 PDT)
Re: [AMBER] Forcefield for RNA
Asfa Ali
(Thu Oct 23 2014 - 04:26:48 PDT)
Re: [AMBER] Forcefield for RNA
David A Case
(Thu Oct 23 2014 - 04:54:12 PDT)
Re: [AMBER] Forcefield for RNA
Jiri Sponer
(Thu Oct 23 2014 - 13:58:58 PDT)
Re: [AMBER] Forcefield for RNA
koushik
(Thu Oct 23 2014 - 14:03:54 PDT)
Re: [AMBER] Forcefield for RNA
koushik
(Thu Oct 23 2014 - 14:06:58 PDT)
Re: [AMBER] Forcefield for RNA
pavel.banas.upol.cz
(Thu Oct 23 2014 - 13:54:28 PDT)
Re: [AMBER] Forcefield for RNA
Jiri Sponer
(Thu Oct 23 2014 - 14:15:20 PDT)
Re: [AMBER] Forcefield for RNA
Asfa Ali
(Fri Oct 24 2014 - 05:46:02 PDT)
Re: [AMBER] Forcefield for RNA
Jason Swails
(Fri Oct 24 2014 - 06:19:43 PDT)
Re: [AMBER] Forcefield for RNA
Asfa Ali
(Sat Oct 25 2014 - 04:19:22 PDT)
[AMBER] loading force field ff14SB
Vlad Cojocaru
(Tue Oct 28 2014 - 08:12:18 PDT)
Re: [AMBER] loading force field ff14SB
Jason Swails
(Tue Oct 28 2014 - 08:36:05 PDT)
Re: [AMBER] loading force field ff14SB
Vlad Cojocaru
(Tue Oct 28 2014 - 08:56:57 PDT)
Re: [AMBER] loading force field ff14SB
Jiri Sponer
(Tue Oct 28 2014 - 09:17:05 PDT)
Re: [AMBER] loading force field ff14SB
Christina Bergonzo
(Tue Oct 28 2014 - 08:31:19 PDT)
[AMBER] peptideligandParameters
zayan alhalabi
(Thu Oct 23 2014 - 01:58:08 PDT)
Re: [AMBER] peptideligandParameters
Jason Swails
(Fri Oct 24 2014 - 05:48:15 PDT)
Re: [AMBER] peptideligandParameters
FyD
(Fri Oct 24 2014 - 22:17:11 PDT)
[AMBER] Number of water hits and density
Suhaib Shekfeh
(Thu Oct 23 2014 - 08:01:05 PDT)
Re: [AMBER] Number of water hits and density
Carlos Simmerling
(Thu Oct 23 2014 - 10:18:00 PDT)
Re: [AMBER] Number of water hits and density
Thomas Cheatham
(Thu Oct 23 2014 - 10:19:06 PDT)
Re: [AMBER] Number of water hits and density
Suhaib Shekfeh
(Sun Oct 26 2014 - 06:50:42 PDT)
[AMBER] MMGBSA doesn't finish
Bernhard Poll
(Thu Oct 23 2014 - 23:22:40 PDT)
Re: [AMBER] MMGBSA doesn't finish
Jason Swails
(Fri Oct 24 2014 - 04:53:10 PDT)
[AMBER] AMBER GAUSSIAN QM/MM
Ayesha Fatima
(Fri Oct 24 2014 - 00:23:29 PDT)
Re: [AMBER] AMBER GAUSSIAN QM/MM
Marc van der Kamp
(Fri Oct 24 2014 - 01:07:50 PDT)
Re: [AMBER] AMBER GAUSSIAN QM/MM
Ayesha Fatima
(Fri Oct 24 2014 - 01:52:46 PDT)
[AMBER] Heme Parameters
杨川
(Fri Oct 24 2014 - 01:08:42 PDT)
Re: [AMBER] Heme Parameters
Jason Swails
(Fri Oct 24 2014 - 04:44:57 PDT)
Re: [AMBER] Heme Parameters
David A Case
(Fri Oct 24 2014 - 05:29:17 PDT)
[AMBER] PDB to P2N conversion
Sylvester Tumusiime
(Sat Oct 25 2014 - 09:14:53 PDT)
Re: [AMBER] PDB to P2N conversion
ABEL Stephane 175950
(Sat Oct 25 2014 - 12:09:28 PDT)
[AMBER] problem with extra-point
Emilio Angelina
(Sat Oct 25 2014 - 09:38:55 PDT)
Re: [AMBER] problem with extra-point
David A Case
(Sat Oct 25 2014 - 13:05:01 PDT)
[AMBER] Temperature not correctly maintained using AMBER14
Gonzalo Jimenez
(Sat Oct 25 2014 - 18:07:38 PDT)
Re: [AMBER] Temperature not correctly maintained using AMBER14
Ross Walker
(Sat Oct 25 2014 - 18:44:59 PDT)
Re: [AMBER] Temperature not correctly maintained using AMBER14
Gonzalo Jimenez
(Sat Oct 25 2014 - 19:41:52 PDT)
Re: [AMBER] Temperature not correctly maintained using AMBER14
Ross Walker
(Sun Oct 26 2014 - 13:22:33 PDT)
Re: [AMBER] Temperature not correctly maintained using AMBER14
Gonzalo Jimenez
(Sun Oct 26 2014 - 14:15:46 PDT)
Re: [AMBER] Temperature not correctly maintained using AMBER14
Ross Walker
(Sun Oct 26 2014 - 18:57:13 PDT)
[AMBER] Problem regarding Chamber
Shubhadip Das
(Sun Oct 26 2014 - 21:28:54 PDT)
Re: [AMBER] Problem regarding Chamber
Jason Swails
(Mon Oct 27 2014 - 09:04:26 PDT)
[AMBER] MMPBSA Error: PB Bomb in pb_atmlist(): maxnba too short
MOHD HOMAIDUR RAHMAN
(Mon Oct 27 2014 - 00:27:34 PDT)
Re: [AMBER] MMPBSA Error: PB Bomb in pb_atmlist(): maxnba too short
Jason Swails
(Mon Oct 27 2014 - 05:19:41 PDT)
[AMBER] Problem regarding Chamber and psf file
Caitlin Scott
(Mon Oct 27 2014 - 06:25:45 PDT)
Re: [AMBER] Problem regarding Chamber and psf file
Jason Swails
(Mon Oct 27 2014 - 06:52:50 PDT)
Re: [AMBER] Problem regarding Chamber and psf file
Caitlin Scott
(Fri Oct 31 2014 - 07:20:04 PDT)
Re: [AMBER] Problem regarding Chamber and psf file
Jason Swails
(Fri Oct 31 2014 - 08:51:40 PDT)
Re: [AMBER] Problem regarding Chamber and psf file
Pete Kekenes-Huskey
(Fri Oct 31 2014 - 13:36:06 PDT)
[AMBER] Running G03
Brittany Boykin
(Mon Oct 27 2014 - 12:14:43 PDT)
Re: [AMBER] Running G03
Kshatresh Dutta Dubey
(Mon Oct 27 2014 - 13:19:53 PDT)
Re: [AMBER] Running G03
FyD
(Mon Oct 27 2014 - 23:50:10 PDT)
[AMBER] GPU enabled Hardware specification
M. Reza Ganjalikhany
(Mon Oct 27 2014 - 13:39:41 PDT)
Re: [AMBER] GPU enabled Hardware specification
Scott Le Grand
(Mon Oct 27 2014 - 14:19:45 PDT)
Re: [AMBER] GPU enabled Hardware specification
M. Reza Ganjalikhany
(Tue Oct 28 2014 - 02:41:10 PDT)
Re: [AMBER] GPU enabled Hardware specification
Jonathan Gough
(Tue Oct 28 2014 - 06:35:20 PDT)
Re: [AMBER] GPU enabled Hardware specification
Jonathan Gough
(Tue Oct 28 2014 - 07:42:41 PDT)
Re: [AMBER] GPU enabled Hardware specification
Ross Walker
(Tue Oct 28 2014 - 07:53:31 PDT)
Re: [AMBER] GPU enabled Hardware specification
M. Reza Ganjalikhany
(Tue Oct 28 2014 - 12:50:36 PDT)
Re: [AMBER] GPU enabled Hardware specification
Scott Le Grand
(Tue Oct 28 2014 - 12:59:37 PDT)
Re: [AMBER] GPU enabled Hardware specification
Ross Walker
(Tue Oct 28 2014 - 14:02:49 PDT)
[AMBER] Regarding Protein-ligand MD
Bikash Ranjan Sahoo
(Mon Oct 27 2014 - 19:58:33 PDT)
Re: [AMBER] Regarding Protein-ligand MD
Robin Betz
(Mon Oct 27 2014 - 20:02:48 PDT)
Re: [AMBER] Regarding Protein-ligand MD
Bikash Ranjan Sahoo
(Mon Oct 27 2014 - 20:17:02 PDT)
Re: [AMBER] Regarding Protein-ligand MD
FyD
(Tue Oct 28 2014 - 02:02:22 PDT)
[AMBER] Problem about "Too many dipole_dipole interactions for allocated" when heat
Ya Gao
(Tue Oct 28 2014 - 19:30:34 PDT)
Re: [AMBER] Problem about "Too many dipole_dipole interactions for allocated" when heat
David A Case
(Wed Oct 29 2014 - 04:38:52 PDT)
Re: [AMBER] Problem about "Too many dipole_dipole interactions for allocated" when heat
Lorenzo Gontrani
(Wed Oct 29 2014 - 04:58:33 PDT)
Re: [AMBER] Problem about "Too many dipole_dipole interactions for allocated" when heat
Ya Gao
(Wed Oct 29 2014 - 05:31:16 PDT)
[AMBER] Entropy calculation
asdda asa
(Tue Oct 28 2014 - 19:38:13 PDT)
Re: [AMBER] Entropy calculation
Jason Swails
(Wed Oct 29 2014 - 10:44:29 PDT)
Re: [AMBER] Entropy calculation
asdda asa
(Wed Oct 29 2014 - 20:31:58 PDT)
Re: [AMBER] How do MCPB make sidechain.bcl?
Saeed Nasiri
(Tue Oct 28 2014 - 21:31:30 PDT)
Re: [AMBER] How do MCPB make sidechain.bcl?
Pengfei Li
(Wed Oct 29 2014 - 12:50:22 PDT)
[AMBER] Problem about "Too many dipole_dipole interactions for allocated" in heat simulation
Tong Zhu
(Tue Oct 28 2014 - 22:23:48 PDT)
[AMBER] problem in DNA-ligand trajectory
Mina Madah
(Wed Oct 29 2014 - 03:54:31 PDT)
Re: [AMBER] problem in DNA-ligand trajectory
Jason Swails
(Wed Oct 29 2014 - 10:22:57 PDT)
[AMBER] Imaging
Sylvester Tumusiime
(Wed Oct 29 2014 - 08:10:36 PDT)
Re: [AMBER] Imaging
Daniel Roe
(Wed Oct 29 2014 - 08:20:16 PDT)
Re: [AMBER] Imaging
Sylvester Tumusiime
(Wed Oct 29 2014 - 08:38:36 PDT)
Re: [AMBER] Imaging
Daniel Roe
(Wed Oct 29 2014 - 08:53:42 PDT)
Re: [AMBER] Imaging
Sylvester Tumusiime
(Wed Oct 29 2014 - 09:11:05 PDT)
Re: [AMBER] Imaging
Sylvester Tumusiime
(Wed Oct 29 2014 - 09:22:13 PDT)
Re: [AMBER] Imaging
Daniel Roe
(Wed Oct 29 2014 - 13:31:17 PDT)
Re: [AMBER] Imaging
Sylvester Tumusiime
(Wed Oct 29 2014 - 14:29:24 PDT)
Re: [AMBER] Imaging
Sylvester Tumusiime
(Thu Oct 30 2014 - 12:23:55 PDT)
Re: [AMBER] Imaging
Thomas Cheatham
(Thu Oct 30 2014 - 13:27:37 PDT)
Re: [AMBER] Imaging
Daniel Roe
(Thu Oct 30 2014 - 13:33:06 PDT)
Re: [AMBER] Imaging
Sylvester Tumusiime
(Thu Oct 30 2014 - 14:51:19 PDT)
[AMBER] restart file position
Fabian Glaser
(Wed Oct 29 2014 - 08:31:42 PDT)
Re: [AMBER] restart file position
Jason Swails
(Wed Oct 29 2014 - 10:17:22 PDT)
[AMBER] Implementing parameterized heme?
Kevin Murphy
(Wed Oct 29 2014 - 10:21:21 PDT)
Re: [AMBER] Implementing parameterized heme?
Pengfei Li
(Wed Oct 29 2014 - 12:35:07 PDT)
Re: [AMBER] Implementing parameterized heme?
Pengfei Li
(Wed Oct 29 2014 - 12:44:02 PDT)
Re: [AMBER] Implementing parameterized heme?
Yarrow Madrona
(Wed Oct 29 2014 - 17:34:21 PDT)
Re: [AMBER] Implementing parameterized heme?
Yarrow Madrona
(Wed Oct 29 2014 - 17:46:23 PDT)
Re: [AMBER] Implementing parameterized heme?
Pengfei Li
(Thu Oct 30 2014 - 12:18:20 PDT)
Re: [AMBER] Implementing parameterized heme?
Pengfei Li
(Thu Oct 30 2014 - 12:15:27 PDT)
[AMBER] using multiple force fields in a simulation
Bhushan
(Thu Oct 30 2014 - 00:45:40 PDT)
Re: [AMBER] using multiple force fields in a simulation
Hannes Loeffler
(Thu Oct 30 2014 - 02:26:37 PDT)
Re: [AMBER] using multiple force fields in a simulation
Carlos Simmerling
(Thu Oct 30 2014 - 08:00:06 PDT)
[AMBER] visualize CPPTRAJ clculated modes
Vlad Cojocaru
(Thu Oct 30 2014 - 02:35:20 PDT)
Re: [AMBER] visualize CPPTRAJ clculated modes
Jason Swails
(Thu Oct 30 2014 - 04:33:21 PDT)
Re: [AMBER] visualize CPPTRAJ clculated modes
Vlad Cojocaru
(Thu Oct 30 2014 - 07:15:50 PDT)
Re: [AMBER] visualize CPPTRAJ clculated modes
Daniel Roe
(Thu Oct 30 2014 - 07:34:28 PDT)
[AMBER] Multiple timecorr commands in one cpptraj script
Eugene Yedvabny
(Thu Oct 30 2014 - 09:54:51 PDT)
Re: [AMBER] Multiple timecorr commands in one cpptraj script
George M Giambasu
(Thu Oct 30 2014 - 11:29:36 PDT)
[AMBER] 3D Histogram in cpptraj
CHAMI F.
(Thu Oct 30 2014 - 10:18:44 PDT)
Re: [AMBER] 3D Histogram in cpptraj
Asaminew Haile
(Thu Oct 30 2014 - 10:25:55 PDT)
Re: [AMBER] 3D Histogram in cpptraj
CHAMI F.
(Thu Oct 30 2014 - 10:31:17 PDT)
Re: [AMBER] 3D Histogram in cpptraj
Daniel Roe
(Fri Oct 31 2014 - 09:53:42 PDT)
[AMBER] pyroglutamic acid or 5-oxoproline
Yves Boulard
(Fri Oct 31 2014 - 04:08:52 PDT)
[AMBER] About geometry of FAD in the F-90 project of http://q4md-forcefieldtools.org/
Emilio Lence
(Fri Oct 31 2014 - 05:47:31 PDT)
[AMBER] Looking force field for beta-peptide
MOHD HOMAIDUR RAHMAN
(Fri Oct 31 2014 - 06:25:54 PDT)
Re: [AMBER] Looking force field for beta-peptide
David A Case
(Fri Oct 31 2014 - 10:26:51 PDT)
Last message date
:
Fri Oct 31 2014 - 14:00:02 PDT
Archived on
: Fri Nov 15 2024 - 05:55:05 PST
456 messages
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