Amber Archive Jan 2016 by author
357 messages
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Starting
Sat Jan 02 2016 - 05:30:02 PST,
Ending
Fri Jan 29 2016 - 15:00:03 PST
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Aishani Prem
[AMBER] Running simulations in parallel
(Mon Jan 25 2016 - 10:19:13 PST)
Alan
Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch
(Thu Jan 14 2016 - 01:13:55 PST)
amin.imtech.res.in
Re: [AMBER] parameters for Mono-methylated Lysine
(Wed Jan 13 2016 - 02:22:45 PST)
ankita mehta
[AMBER] Dear All
(Sat Jan 23 2016 - 06:49:59 PST)
anu chandra
Re: [AMBER] Help to choose best-fit ion model
(Fri Jan 29 2016 - 14:56:07 PST)
[AMBER] Help to choose best-fit ion model
(Fri Jan 29 2016 - 06:26:39 PST)
[AMBER] cpptraj molsurf error
(Wed Jan 27 2016 - 04:23:06 PST)
Re: [AMBER] Right metal ion model
(Tue Jan 26 2016 - 11:41:44 PST)
[AMBER] Right metal ion model
(Tue Jan 26 2016 - 08:34:26 PST)
Re: [AMBER] Angle calculation between two structures
(Fri Jan 15 2016 - 12:12:52 PST)
Re: [AMBER] contact analysis with CPPTRAJ
(Fri Jan 15 2016 - 09:25:41 PST)
Re: [AMBER] Angle calculation between two structures
(Fri Jan 15 2016 - 09:24:55 PST)
[AMBER] Angle calculation between two structures
(Fri Jan 15 2016 - 04:58:21 PST)
[AMBER] contact analysis with CPPTRAJ
(Fri Jan 15 2016 - 03:59:04 PST)
Asmita Gupta
Re: [AMBER] free energy calculation of folding
(Fri Jan 29 2016 - 00:50:05 PST)
[AMBER] free energy calculation of folding
(Thu Jan 28 2016 - 04:14:33 PST)
Barbault Florent
Re: [AMBER] PMF
(Sun Jan 03 2016 - 01:09:16 PST)
Benjamin D Madej
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Tue Jan 19 2016 - 13:26:36 PST)
Bill Ross
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Thu Jan 21 2016 - 20:09:10 PST)
Re: [AMBER] Problem with Tleap
(Thu Jan 21 2016 - 18:41:59 PST)
Re: [AMBER] Fail to start nab
(Mon Jan 18 2016 - 02:44:35 PST)
Re: [AMBER] How to maintain planerity of graphene sheets
(Thu Jan 14 2016 - 00:38:18 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Mon Jan 11 2016 - 15:18:51 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Mon Jan 11 2016 - 12:02:20 PST)
Re: [AMBER] Errors during Building Sidechain Model（MCPB program）
(Wed Jan 06 2016 - 21:25:22 PST)
Re: [AMBER] Errors during Building Sidechain Model（MCPB program）
(Wed Jan 06 2016 - 20:47:49 PST)
Re: [AMBER] PMF
(Sat Jan 02 2016 - 22:49:56 PST)
Bin Wang
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Fri Jan 22 2016 - 17:58:13 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Thu Jan 21 2016 - 20:03:16 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Tue Jan 19 2016 - 13:46:35 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Tue Jan 19 2016 - 12:11:43 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Tue Jan 19 2016 - 10:40:45 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Tue Jan 19 2016 - 06:50:12 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Mon Jan 18 2016 - 20:11:39 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Mon Jan 11 2016 - 21:52:16 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Mon Jan 11 2016 - 14:50:41 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Mon Jan 11 2016 - 11:55:43 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Mon Jan 11 2016 - 08:26:02 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Mon Jan 11 2016 - 07:45:42 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Mon Jan 11 2016 - 07:41:21 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Mon Jan 11 2016 - 07:40:23 PST)
[AMBER] Problem when using lipid14 force filed in Amber 11
(Sat Jan 09 2016 - 14:40:26 PST)
Carlos Romero
Re: [AMBER] cuda info
(Sun Jan 24 2016 - 09:08:17 PST)
[AMBER] cuda info
(Sat Jan 23 2016 - 22:46:30 PST)
Carlos Simmerling
Re: [AMBER] free energy calculation of folding
(Fri Jan 29 2016 - 07:15:13 PST)
Re: [AMBER] atom clash and close contact after MD simulation in water
(Wed Jan 27 2016 - 06:33:36 PST)
Re: [AMBER] restraints in simulations
(Tue Jan 26 2016 - 08:53:48 PST)
Re: [AMBER] Improving the quality of the model
(Wed Jan 20 2016 - 05:31:41 PST)
Re: [AMBER] PMF
(Sun Jan 03 2016 - 05:05:23 PST)
case
Re: [AMBER] Problem with Tleap
(Thu Jan 21 2016 - 19:03:06 PST)
chemjxn
[AMBER] MCPB.py error
(Thu Jan 21 2016 - 22:48:51 PST)
Chris
[AMBER] Question about LJ_1264 for Eu3+?
(Tue Jan 26 2016 - 07:15:24 PST)
[AMBER] hbond and image problem in cpptraj
(Wed Jan 06 2016 - 19:46:03 PST)
Chris
Re: [AMBER] hbond and image problem in cpptraj
(Thu Jan 07 2016 - 10:50:18 PST)
Chris Moth
Re: [AMBER] Howto cpptraj - multiple trajin-commands in one line
(Thu Jan 14 2016 - 08:43:09 PST)
Re: [AMBER] Howto cpptraj - multiple trajin-commands in one line
(Thu Jan 14 2016 - 07:40:23 PST)
Christian Schafmeister
[AMBER] Iron/ligand parameters for AMBER
(Tue Jan 26 2016 - 06:55:20 PST)
[AMBER] What is the most modern AMBER parm/top format?
(Fri Jan 22 2016 - 07:58:31 PST)
Christina Bergonzo
Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15
(Sat Jan 23 2016 - 05:33:03 PST)
Re: [AMBER] format of seconday structure calculation by cpptraj
(Sun Jan 17 2016 - 06:29:47 PST)
Covington, Cody Lance
[AMBER] setup for non-periodic system
(Tue Jan 26 2016 - 13:01:00 PST)
Damiano Spadoni
Re: [AMBER] g03 error message
(Mon Jan 25 2016 - 02:58:13 PST)
Re: [AMBER] g03 error message
(Mon Jan 25 2016 - 02:10:08 PST)
[AMBER] g03 error message
(Sun Jan 24 2016 - 10:15:49 PST)
Daniel Roe
Re: [AMBER] Cpptraj Filter of Radius of gyration
(Fri Jan 29 2016 - 07:35:14 PST)
Re: [AMBER] cpptraj molsurf error
(Wed Jan 27 2016 - 10:26:52 PST)
Re: [AMBER] RMSD w.r.t reference structure
(Wed Jan 27 2016 - 06:53:22 PST)
Re: [AMBER] Running simulations in parallel
(Mon Jan 25 2016 - 11:03:59 PST)
Re: [AMBER] Error: A residue defined as a "fast 3-point water"
(Fri Jan 22 2016 - 07:18:06 PST)
Re: [AMBER] Angle calculation between two structures
(Fri Jan 15 2016 - 10:28:19 PST)
Re: [AMBER] contact analysis with CPPTRAJ
(Fri Jan 15 2016 - 08:12:24 PST)
Re: [AMBER] Angle calculation between two structures
(Fri Jan 15 2016 - 07:59:52 PST)
Re: [AMBER] Howto cpptraj - multiple trajin-commands in one line
(Thu Jan 14 2016 - 12:49:21 PST)
Re: [AMBER] Howto cpptraj - multiple trajin-commands in one line
(Thu Jan 14 2016 - 08:15:11 PST)
Re: [AMBER] Contact analysis using cpptraj
(Wed Jan 13 2016 - 09:10:15 PST)
Re: [AMBER] RMSD selected residues
(Wed Jan 13 2016 - 08:51:25 PST)
Re: [AMBER] hbond and image problem in cpptraj
(Thu Jan 07 2016 - 09:50:45 PST)
Re: [AMBER] Problems with tleap when generating gib structures
(Tue Jan 05 2016 - 11:05:52 PST)
David A Case
Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15
(Sat Jan 23 2016 - 12:52:56 PST)
Re: [AMBER] Dear All
(Sat Jan 23 2016 - 12:51:21 PST)
Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15
(Sat Jan 23 2016 - 07:02:19 PST)
Re: [AMBER] Error: A residue defined as a "fast 3-point water"
(Fri Jan 22 2016 - 05:13:06 PST)
Re: [AMBER] problem with reduce and energy minimization
(Thu Jan 21 2016 - 04:53:40 PST)
Re: [AMBER] Fwd: High RMSD values due to use of iwrap
(Wed Jan 20 2016 - 05:06:05 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Tue Jan 19 2016 - 09:05:21 PST)
Re: [AMBER] python error when using pdb4amber
(Tue Jan 19 2016 - 05:00:24 PST)
Re: [AMBER] Parameter and coordinate files
(Mon Jan 18 2016 - 05:02:08 PST)
Re: [AMBER] Problem installing AmberTools1.5 on Mac OS X 10.11 EL Capitan
(Fri Jan 15 2016 - 09:02:55 PST)
Re: [AMBER] System becomes unstable upon heating
(Thu Jan 14 2016 - 04:38:21 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Tue Jan 12 2016 - 05:49:06 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Mon Jan 11 2016 - 08:59:13 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Mon Jan 11 2016 - 08:46:32 PST)
Re: [AMBER] premed.MPI warning
(Sun Jan 10 2016 - 05:45:10 PST)
Re: [AMBER] Dr Baliram Lone
(Sat Jan 09 2016 - 05:58:55 PST)
Re: [AMBER] High RMSD values due to use of iwrap
(Fri Jan 08 2016 - 06:07:59 PST)
Re: [AMBER] how to make active site conserve water unique before loading pdb on xleap?
(Fri Jan 08 2016 - 06:01:54 PST)
Re: [AMBER] Error in running AMBER 12 GPU simulations[application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0]
(Thu Jan 07 2016 - 05:08:52 PST)
Re: [AMBER] ligand topology genaration
(Thu Jan 07 2016 - 05:04:12 PST)
Re: [AMBER] xleap : adding ions out of box
(Wed Jan 06 2016 - 04:53:09 PST)
Re: [AMBER] Problems with tleap when generating gib structures
(Tue Jan 05 2016 - 05:25:52 PST)
Re: [AMBER] ligand topology genaration
(Tue Jan 05 2016 - 05:20:39 PST)
Re: [AMBER] Active site conserve water issue.
(Sat Jan 02 2016 - 07:05:29 PST)
David Case
Re: [AMBER] Parameter and coordinate files
(Sat Jan 16 2016 - 19:17:00 PST)
David Mayes
Re: [AMBER] KeyError - MCPB.py tutorial
(Fri Jan 29 2016 - 01:20:15 PST)
Re: [AMBER] KeyError - MCPB.py tutorial
(Tue Jan 26 2016 - 07:43:26 PST)
Re: [AMBER] KeyError - MCPB.py tutorial
(Tue Jan 26 2016 - 06:01:37 PST)
Re: [AMBER] KeyError - MCPB.py tutorial
(Mon Jan 25 2016 - 07:04:53 PST)
[AMBER] KeyError - MCPB.py tutorial
(Fri Jan 22 2016 - 05:25:07 PST)
Dr Baliram lone
[AMBER] Dr Baliram Lone
(Sat Jan 09 2016 - 00:31:38 PST)
Eiros Zamora, Juan
Re: [AMBER] Scripting CPPTRAJ Analysis Commands within a PBS Script
(Sun Jan 10 2016 - 03:56:58 PST)
Ekaterina Ratkova
Re: [AMBER] Problem installing AmberTools1.5 on Mac OS X 10.11 EL Capitan
(Mon Jan 18 2016 - 02:27:21 PST)
Re: [AMBER] Problem installing AmberTools1.5 on Mac OS X 10.11 EL Capitan
(Fri Jan 15 2016 - 07:39:38 PST)
[AMBER] Fwd: Problem installing AmberTools1.5 on Mac OS X 10.11 EL Capitan
(Fri Jan 15 2016 - 04:21:21 PST)
[AMBER] Problem installing AmberTools1.5 on Mac OS X 10.11 EL Capitan
(Fri Jan 15 2016 - 04:15:05 PST)
elham sattarinezhad
[AMBER] mmpbsa calculation
(Tue Jan 12 2016 - 02:53:53 PST)
Elisa Frezza
[AMBER] Fwd: arrêt de travail
(Wed Jan 06 2016 - 05:40:06 PST)
Elisa Pieri
Re: [AMBER] How to put ACE and NME on the ends of a missing loop
(Fri Jan 22 2016 - 07:02:46 PST)
[AMBER] How to put ACE and NME on the ends of a missing loop
(Fri Jan 22 2016 - 05:20:39 PST)
Re: [AMBER] python error when using pdb4amber
(Thu Jan 21 2016 - 01:15:03 PST)
Re: [AMBER] python error when using pdb4amber
(Tue Jan 19 2016 - 00:38:42 PST)
[AMBER] python error when using pdb4amber
(Mon Jan 18 2016 - 04:34:15 PST)
[AMBER] Problem with A08 tutorial, solvateBox error
(Thu Jan 14 2016 - 04:41:12 PST)
Fabian gmail
[AMBER] shape of a peptide array
(Mon Jan 04 2016 - 03:54:34 PST)
Falko Jähnert
Re: [AMBER] Howto cpptraj - multiple trajin-commands in one line
(Wed Jan 20 2016 - 07:37:09 PST)
[AMBER] Howto cpptraj - multiple trajin-commands in one line
(Thu Jan 14 2016 - 04:25:22 PST)
FyD
[AMBER] q4md-forcefieldtools is back with new features
(Tue Jan 05 2016 - 22:09:20 PST)
George Tzotzos
[AMBER] General question on applying restraints during production MD
(Tue Jan 26 2016 - 02:16:26 PST)
Re: [AMBER] premed.MPI warning
(Mon Jan 11 2016 - 18:44:27 PST)
Re: [AMBER] premed.MPI warning
(Mon Jan 11 2016 - 15:26:12 PST)
Re: [AMBER] premed.MPI warning
(Mon Jan 11 2016 - 08:23:28 PST)
Re: [AMBER] premed.MPI warning
(Sun Jan 10 2016 - 12:38:39 PST)
[AMBER] premed.MPI warning
(Sun Jan 10 2016 - 02:37:45 PST)
Guqin Shi
Re: [AMBER] MMPBSA Job Parallel Running
(Fri Jan 15 2016 - 06:29:36 PST)
Re: [AMBER] MMPBSA Job Parallel Running
(Thu Jan 14 2016 - 08:47:54 PST)
Re: [AMBER] MMPBSA Job Parallel Running
(Wed Jan 13 2016 - 07:56:45 PST)
Re: [AMBER] MMPBSA Job Parallel Running
(Wed Jan 13 2016 - 07:46:55 PST)
[AMBER] MMPBSA Job Parallel Running
(Mon Jan 11 2016 - 11:29:39 PST)
Hai Nguyen
Re: [AMBER] Howto cpptraj - multiple trajin-commands in one line
(Thu Jan 14 2016 - 15:08:25 PST)
Re: [AMBER] Kinetic Energy
(Wed Jan 13 2016 - 18:31:16 PST)
Re: [AMBER] Kinetic Energy
(Wed Jan 13 2016 - 18:03:53 PST)
Hannes Loeffler
Re: [AMBER] PCA
(Wed Jan 27 2016 - 01:40:26 PST)
Re: [AMBER] g03 error message
(Mon Jan 25 2016 - 02:38:11 PST)
Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch
(Wed Jan 13 2016 - 09:04:23 PST)
Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch
(Wed Jan 13 2016 - 07:03:10 PST)
Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch
(Wed Jan 13 2016 - 06:20:27 PST)
Re: [AMBER] parameters for Mono-methylated Lysine
(Wed Jan 13 2016 - 03:03:58 PST)
Re: [AMBER] mmpbsa calculation
(Tue Jan 12 2016 - 03:08:38 PST)
hannes.loeffler.stfc.ac.uk
Re: [AMBER] g03 error message
(Sun Jan 24 2016 - 11:12:20 PST)
Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15
(Sat Jan 23 2016 - 03:59:12 PST)
Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15
(Sat Jan 23 2016 - 03:35:02 PST)
Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15
(Sat Jan 23 2016 - 03:23:23 PST)
Re: [AMBER] Remove single water molecule using thermodynamic integration
(Fri Jan 08 2016 - 00:39:39 PST)
Himanshu Joshi
Re: [AMBER] xleap : adding ions out of box
(Fri Jan 08 2016 - 02:50:17 PST)
Re: [AMBER] xleap : adding ions out of box
(Wed Jan 06 2016 - 10:22:10 PST)
[AMBER] xleap : adding ions out of box
(Tue Jan 05 2016 - 23:45:48 PST)
Indrajit Deb
[AMBER] problem with pmemd.cuda and PBS
(Mon Jan 11 2016 - 05:52:32 PST)
InSuk Joung
Re: [AMBER] parmed question regarding modifying Lennard-Jones parameters
(Fri Jan 08 2016 - 06:00:01 PST)
[AMBER] parmed question regarding modifying Lennard-Jones parameters
(Fri Jan 08 2016 - 00:45:03 PST)
Irfan Alibay
[AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15
(Sat Jan 23 2016 - 14:07:18 PST)
[AMBER] premed.MPI warning
(Tue Jan 12 2016 - 08:34:21 PST)
[AMBER] premed.MPI warning
(Tue Jan 12 2016 - 07:44:01 PST)
Jacopo Sgrignani
Re: [AMBER] atom clash and close contact after MD simulation in water
(Wed Jan 27 2016 - 06:03:05 PST)
jagannath mondal
[AMBER] How to maintain planerity of graphene sheets
(Wed Jan 13 2016 - 23:16:34 PST)
Jason Swails
Re: [AMBER] Error Message
(Fri Jan 29 2016 - 07:05:16 PST)
Re: [AMBER] free energy calculation of folding
(Fri Jan 29 2016 - 07:02:17 PST)
Re: [AMBER] free energy calculation of folding
(Thu Jan 28 2016 - 08:55:17 PST)
Re: [AMBER] two elongated bonds while visualuizing prmtop and inprcd in vmd
(Wed Jan 27 2016 - 06:03:59 PST)
Re: [AMBER] setup for non-periodic system
(Tue Jan 26 2016 - 14:26:13 PST)
Re: [AMBER] restraints in simulations
(Tue Jan 26 2016 - 07:49:26 PST)
Re: [AMBER] General question on applying restraints during production MD
(Tue Jan 26 2016 - 04:57:58 PST)
Re: [AMBER] restraints in simulations
(Tue Jan 26 2016 - 04:50:18 PST)
Re: [AMBER] Running simulations in parallel
(Mon Jan 25 2016 - 14:32:45 PST)
Re: [AMBER] troubles in understanding, amber minimization input
(Sun Jan 24 2016 - 18:19:06 PST)
Re: [AMBER] troubles in understanding, amber minimization input
(Sun Jan 24 2016 - 04:54:53 PST)
Re: [AMBER] Dear All
(Sat Jan 23 2016 - 17:16:45 PST)
Re: [AMBER] What is the most modern AMBER parm/top format?
(Fri Jan 22 2016 - 09:19:04 PST)
Re: [AMBER] PCA analysis
(Fri Jan 22 2016 - 05:09:35 PST)
Re: [AMBER] use of LIE command
(Fri Jan 22 2016 - 05:03:26 PST)
Re: [AMBER] Error: A residue defined as a "fast 3-point water"
(Fri Jan 22 2016 - 04:59:07 PST)
Re: [AMBER] Stability Calculation using MMPBSA.py
(Fri Jan 22 2016 - 04:49:52 PST)
Re: [AMBER] MMPBSA for apo-proteins
(Thu Jan 21 2016 - 11:50:06 PST)
Re: [AMBER] Amber14 Installation with cuda
(Thu Jan 21 2016 - 06:56:01 PST)
Re: [AMBER] python error when using pdb4amber
(Tue Jan 19 2016 - 06:00:46 PST)
Re: [AMBER] python error when using pdb4amber
(Tue Jan 19 2016 - 05:47:50 PST)
Re: [AMBER] python error when using pdb4amber
(Mon Jan 18 2016 - 13:24:04 PST)
Re: [AMBER] Completely fixed atoms in MD Simulation (pmemd)
(Mon Jan 18 2016 - 13:12:16 PST)
Re: [AMBER] Need Help regarding Energy Calculation
(Mon Jan 18 2016 - 07:06:54 PST)
Re: [AMBER] cpptraj question
(Sat Jan 16 2016 - 09:55:00 PST)
Re: [AMBER] Problem installing AmberTools1.5 on Mac OS X 10.11 EL Capitan
(Fri Jan 15 2016 - 07:28:45 PST)
Re: [AMBER] Problem with A08 tutorial, solvateBox error
(Thu Jan 14 2016 - 20:12:04 PST)
Re: [AMBER] Questions about Steered MD in Amber
(Thu Jan 14 2016 - 20:04:56 PST)
Re: [AMBER] MMPBSA Job Parallel Running
(Thu Jan 14 2016 - 19:57:39 PST)
Re: [AMBER] Kinetic Energy
(Wed Jan 13 2016 - 16:42:03 PST)
Re: [AMBER] System becomes unstable upon heating
(Wed Jan 13 2016 - 08:50:24 PST)
Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch
(Wed Jan 13 2016 - 08:43:47 PST)
Re: [AMBER] MMPBSA Job Parallel Running
(Wed Jan 13 2016 - 08:40:45 PST)
Re: [AMBER] MMPBSA Job Parallel Running
(Wed Jan 13 2016 - 08:40:12 PST)
Re: [AMBER] premed.MPI warning
(Tue Jan 12 2016 - 08:54:58 PST)
Re: [AMBER] premed.MPI warning
(Tue Jan 12 2016 - 08:05:47 PST)
Re: [AMBER] ligand topology genaration
(Tue Jan 12 2016 - 04:28:02 PST)
Re: [AMBER] premed.MPI warning
(Mon Jan 11 2016 - 16:46:16 PST)
Re: [AMBER] problem with pmemd.cuda and PBS
(Mon Jan 11 2016 - 06:01:16 PST)
Re: [AMBER] premed.MPI warning
(Mon Jan 11 2016 - 05:12:47 PST)
Re: [AMBER] premed.MPI warning
(Sun Jan 10 2016 - 08:43:33 PST)
Re: [AMBER] parmed question regarding modifying Lennard-Jones parameters
(Fri Jan 08 2016 - 06:08:43 PST)
Re: [AMBER] parmed question regarding modifying Lennard-Jones parameters
(Fri Jan 08 2016 - 03:50:18 PST)
Re: [AMBER] High RMSD values due to use of iwrap
(Fri Jan 08 2016 - 03:44:11 PST)
Re: [AMBER] ligand topology genaration
(Thu Jan 07 2016 - 05:21:35 PST)
Re: [AMBER] Help: parameters of Equilibration and production scripts
(Thu Jan 07 2016 - 03:59:45 PST)
Re: [AMBER] ligand topology genaration
(Thu Jan 07 2016 - 03:52:05 PST)
Re: [AMBER] How to appropriately replace the amber force in the source codes ?
(Wed Jan 06 2016 - 06:02:51 PST)
Re: [AMBER] MMPBSA_Error: Could not find necessary program [mmpbsa_py_energy]
(Wed Jan 06 2016 - 04:25:34 PST)
Re: [AMBER] ligand topology genaration
(Wed Jan 06 2016 - 04:24:28 PST)
Re: [AMBER] Problems with tleap when generating gib structures
(Tue Jan 05 2016 - 08:57:39 PST)
Re: [AMBER] ligand topology genaration
(Tue Jan 05 2016 - 04:38:52 PST)
Re: [AMBER] Fwd: Requesting clarifications about QM/MM minimization
(Tue Jan 05 2016 - 04:34:35 PST)
Re: [AMBER] pH dependent calculation for Oligomers
(Tue Jan 05 2016 - 04:29:27 PST)
Re: [AMBER] pH dependent calculation for Oligomers
(Mon Jan 04 2016 - 03:02:46 PST)
Re: [AMBER] Convert gromacs output file to Amber format
(Sun Jan 03 2016 - 07:01:12 PST)
JEAN MARC BILLOD
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Mon Jan 11 2016 - 12:17:47 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Mon Jan 11 2016 - 08:33:46 PST)
Jean-Marc
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Mon Jan 11 2016 - 21:25:51 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Sun Jan 10 2016 - 21:34:18 PST)
Jean-Marc Billod
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Mon Jan 18 2016 - 21:46:51 PST)
Re: [AMBER] Howto cpptraj - multiple trajin-commands in one line
(Thu Jan 14 2016 - 07:40:35 PST)
jinfeng liu
Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15
(Sat Jan 23 2016 - 03:49:38 PST)
Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15
(Sat Jan 23 2016 - 03:27:41 PST)
[AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15
(Sat Jan 23 2016 - 03:10:34 PST)
[AMBER] How to appropriately replace the amber force in the source codes ?
(Wed Jan 06 2016 - 05:37:46 PST)
Johannes Loeffler
Re: [AMBER] Remove single water molecule using thermodynamic integration
(Fri Jan 08 2016 - 00:41:52 PST)
[AMBER] Remove single water molecule using thermodynamic integration
(Fri Jan 08 2016 - 00:10:09 PST)
josephine
[AMBER] Cpptraj Filter of Radius of gyration
(Fri Jan 29 2016 - 07:02:19 PST)
Josh Berryman
[AMBER] 3DRISM: erratic values for partial molar volume
(Wed Jan 27 2016 - 02:05:15 PST)
Re: [AMBER] shape of a peptide array
(Wed Jan 13 2016 - 02:34:18 PST)
Jérémie KNOOPS [531802]
[AMBER] Problems when trying to improve angle parameters whith paramfit
(Mon Jan 18 2016 - 04:45:29 PST)
Karl Kirschner
Re: [AMBER] parameters for Mono-methylated Lysine
(Wed Jan 13 2016 - 02:20:23 PST)
kenfack cyril
Re: [AMBER] troubles in understanding, amber minimization input
(Mon Jan 25 2016 - 00:00:27 PST)
Kenneth Huang
Re: [AMBER] Problem with A08 tutorial, solvateBox error
(Thu Jan 14 2016 - 06:36:17 PST)
Re: [AMBER] MMPBSA Job Parallel Running
(Mon Jan 11 2016 - 14:10:35 PST)
Re: [AMBER] Scripting CPPTRAJ Analysis Commands within a PBS Script
(Sun Jan 10 2016 - 09:00:54 PST)
Khabiri, Morteza
[AMBER] aMD with two component
(Fri Jan 29 2016 - 10:26:47 PST)
Kucharski Jr., Amir N
[AMBER] MMPBSA for apo-proteins
(Thu Jan 21 2016 - 10:56:23 PST)
[AMBER] Contact analysis using cpptraj
(Wed Jan 13 2016 - 07:25:22 PST)
Lara rajam
Re: [AMBER] restraints in simulations
(Tue Jan 26 2016 - 10:08:56 PST)
Re: [AMBER] restraints in simulations
(Tue Jan 26 2016 - 07:27:42 PST)
[AMBER] restraints in simulations
(Mon Jan 25 2016 - 10:23:04 PST)
Levan Tsereteli
Re: [AMBER] Problems with tleap when generating gib structures
(Tue Jan 05 2016 - 11:11:51 PST)
Re: [AMBER] Problems with tleap when generating gib structures
(Tue Jan 05 2016 - 10:11:18 PST)
Re: [AMBER] Problems with tleap when generating gib structures
(Tue Jan 05 2016 - 08:51:12 PST)
Re: [AMBER] Problems with tleap when generating gib structures
(Tue Jan 05 2016 - 06:26:07 PST)
[AMBER] Problems with tleap when generating gib structures
(Tue Jan 05 2016 - 03:36:32 PST)
Lorenzo Gontrani
Re: [AMBER] Convert gromacs output file to Amber format
(Sun Jan 03 2016 - 09:15:26 PST)
Luis Esteban
[AMBER] FW: Problem with Tleap
(Thu Jan 21 2016 - 21:07:31 PST)
[AMBER] Problem with Tleap
(Thu Jan 21 2016 - 17:00:47 PST)
Manjula Saravanan
[AMBER] Sander minimization of protein-ligand complex
(Tue Jan 05 2016 - 21:21:23 PST)
[AMBER] Fwd: Requesting clarifications about QM/MM minimization
(Mon Jan 04 2016 - 21:39:25 PST)
Marcelo Andrade Chagas
Re: [AMBER] Problem with Tleap
(Thu Jan 21 2016 - 17:42:46 PST)
Re: [AMBER] Problem with Tleap
(Thu Jan 21 2016 - 17:20:37 PST)
Maryam Hamzehee
Re: [AMBER] problem with reduce and energy minimization
(Sun Jan 24 2016 - 01:59:04 PST)
[AMBER] problem with reduce and energy minimization
(Wed Jan 20 2016 - 23:55:38 PST)
Melisa Averina
[AMBER] Completely fixed atoms in MD Simulation (pmemd)
(Mon Jan 18 2016 - 12:03:36 PST)
Mijiddorj Batsaikhan
Re: [AMBER] pH dependent calculation for Oligomers
(Tue Jan 05 2016 - 00:42:25 PST)
[AMBER] pH dependent calculation for Oligomers
(Mon Jan 04 2016 - 02:19:06 PST)
Mohan Pradhan
[AMBER] exact values corresponding to the grid points in GIST calculations
(Sat Jan 09 2016 - 02:36:25 PST)
neha chaudhary
Re: [AMBER] ligand topology genaration
(Tue Jan 12 2016 - 03:35:31 PST)
Re: [AMBER] ligand topology genaration
(Thu Jan 07 2016 - 04:26:38 PST)
Re: [AMBER] ligand topology genaration
(Wed Jan 06 2016 - 21:33:36 PST)
Re: [AMBER] ligand topology genaration
(Wed Jan 06 2016 - 01:25:04 PST)
[AMBER] ligand topology genaration
(Tue Jan 05 2016 - 02:24:34 PST)
Re: [AMBER] Convert gromacs output file to Amber format
(Sun Jan 03 2016 - 21:13:39 PST)
[AMBER] Convert gromacs output file to Amber format
(Sun Jan 03 2016 - 00:40:16 PST)
Nida Baig
[AMBER] two elongated bonds while visualuizing prmtop and inprcd in vmd
(Wed Jan 27 2016 - 03:05:38 PST)
Nikolay N. Kuzmich
[AMBER] Fail to start nab
(Mon Jan 18 2016 - 02:32:53 PST)
Pallavi Mohanty
Re: [AMBER] MMPBSA Job Parallel Running
(Mon Jan 11 2016 - 20:41:59 PST)
[AMBER] MMPBSA_Error: Could not find necessary program [mmpbsa_py_energy]
(Tue Jan 05 2016 - 23:48:37 PST)
Pengfei Li
Re: [AMBER] Help to choose best-fit ion model
(Fri Jan 29 2016 - 07:15:26 PST)
Re: [AMBER] KeyError - MCPB.py tutorial
(Fri Jan 29 2016 - 07:06:54 PST)
Re: [AMBER] KeyError - MCPB.py tutorial
(Thu Jan 28 2016 - 09:08:43 PST)
Re: [AMBER] Question about LJ_1264 for Eu3+?
(Tue Jan 26 2016 - 08:45:21 PST)
Re: [AMBER] Right metal ion model
(Tue Jan 26 2016 - 08:39:13 PST)
Re: [AMBER] KeyError - MCPB.py tutorial
(Tue Jan 26 2016 - 07:40:49 PST)
Re: [AMBER] KeyError - MCPB.py tutorial
(Mon Jan 25 2016 - 14:49:49 PST)
Re: [AMBER] KeyError - MCPB.py tutorial
(Fri Jan 22 2016 - 08:10:15 PST)
Re: [AMBER] MCPB.py error
(Fri Jan 22 2016 - 08:08:52 PST)
Re: [AMBER] MCPB Step 2s help
(Tue Jan 12 2016 - 09:16:00 PST)
Rasha Alqus
[AMBER] PMF
(Sat Jan 02 2016 - 22:34:59 PST)
Ratkova, Ekaterina, Dr.
[AMBER] Problem installing AmberTools1.5 on Mac OS X 10.11 EL Capitan
(Fri Jan 15 2016 - 04:53:42 PST)
richa anand
[AMBER] RMSD w.r.t reference structure
(Wed Jan 27 2016 - 01:24:02 PST)
[AMBER] PCA
(Wed Jan 27 2016 - 01:18:11 PST)
[AMBER] PCA analysis
(Fri Jan 22 2016 - 04:18:53 PST)
[AMBER] use of LIE command
(Fri Jan 22 2016 - 04:08:06 PST)
[AMBER] Fwd: High RMSD values due to use of iwrap
(Tue Jan 19 2016 - 21:42:24 PST)
[AMBER] High RMSD values due to use of iwrap
(Fri Jan 08 2016 - 03:09:12 PST)
Robert Molt
Re: [AMBER] Problem with Tleap
(Thu Jan 21 2016 - 17:31:35 PST)
[AMBER] cpptraj question
(Sat Jan 16 2016 - 08:38:36 PST)
Re: [AMBER] Scripting CPPTRAJ Analysis Commands within a PBS Script
(Sun Jan 10 2016 - 19:10:12 PST)
[AMBER] Scripting CPPTRAJ Analysis Commands within a PBS Script
(Sat Jan 09 2016 - 21:12:53 PST)
Ross Walker
Re: [AMBER] cuda info
(Sat Jan 23 2016 - 23:39:13 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Tue Jan 19 2016 - 13:05:46 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Tue Jan 19 2016 - 11:06:51 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Tue Jan 19 2016 - 07:43:40 PST)
Re: [AMBER] premed.MPI warning
(Mon Jan 11 2016 - 18:35:11 PST)
Re: [AMBER] Problem when using lipid14 force filed in Amber 11
(Mon Jan 11 2016 - 08:18:16 PST)
Re: [AMBER] premed.MPI warning
(Mon Jan 11 2016 - 08:14:28 PST)
Re: [AMBER] premed.MPI warning
(Sun Jan 10 2016 - 10:20:26 PST)
Saikat Dutta chowdhury
[AMBER] Stability Calculation using MMPBSA.py
(Fri Jan 22 2016 - 02:08:25 PST)
Re: [AMBER] Need Help regarding Energy Calculation
(Mon Jan 18 2016 - 19:49:29 PST)
[AMBER] Need Help regarding Energy Calculation
(Mon Jan 18 2016 - 03:57:46 PST)
Saman Yousuf ali
[AMBER] troubles in understanding, amber minimization input
(Sun Jan 24 2016 - 01:51:32 PST)
Re: [AMBER] Error: A residue defined as a "fast 3-point water"
(Fri Jan 22 2016 - 06:29:59 PST)
[AMBER] Error: A residue defined as a "fast 3-point water"
(Fri Jan 22 2016 - 03:28:34 PST)
[AMBER] how to make active site conserve water unique before loading pdb on xleap?
(Thu Jan 07 2016 - 11:11:36 PST)
[AMBER] Active site conserve water issue.
(Sat Jan 02 2016 - 05:24:31 PST)
Sangita Kachhap
Re: [AMBER] format of seconday structure calculation by cpptraj
(Sun Jan 17 2016 - 06:28:23 PST)
[AMBER] format of seconday structure calculation by cpptraj
(Sun Jan 17 2016 - 05:26:21 PST)
Sarah Graham
[AMBER] Amber 12 GTX-980
(Thu Jan 21 2016 - 07:07:48 PST)
Sehrish Naz
[AMBER] Help: parameters of Equilibration and production scripts
(Wed Jan 06 2016 - 22:05:43 PST)
Sergey Samsonov
Re: [AMBER] Enthalpy of solute+solvent
(Tue Jan 19 2016 - 00:42:39 PST)
[AMBER] Enthalpy of solute+solvent
(Mon Jan 18 2016 - 07:12:54 PST)
Sidney Elmer
[AMBER] Run your Amber simulations in the cloud with Rescale
(Fri Jan 22 2016 - 08:45:27 PST)
Stefano Sarao S215563
Re: [AMBER] Parameter and coordinate files
(Sun Jan 17 2016 - 02:50:05 PST)
[AMBER] Parameter and coordinate files
(Sat Jan 16 2016 - 11:12:47 PST)
Steven Ramsey
Re: [AMBER] exact values corresponding to the grid points in GIST calculations
(Sat Jan 09 2016 - 15:29:14 PST)
Sudip Das
Re: [AMBER] System becomes unstable upon heating
(Wed Jan 13 2016 - 20:31:54 PST)
[AMBER] System becomes unstable upon heating
(Wed Jan 13 2016 - 07:19:47 PST)
Sushi Shilpa
[AMBER] Improving the quality of the model
(Tue Jan 19 2016 - 22:50:23 PST)
tarak karmakar
Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch
(Fri Jan 15 2016 - 08:44:14 PST)
Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch
(Wed Jan 13 2016 - 09:42:35 PST)
Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch
(Wed Jan 13 2016 - 06:39:13 PST)
[AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch
(Wed Jan 13 2016 - 05:42:37 PST)
Tavenor, Nathan Albert
Re: [AMBER] MCPB Step 2s help
(Wed Jan 13 2016 - 04:49:47 PST)
[AMBER] MCPB Step 2s help
(Mon Jan 11 2016 - 12:30:42 PST)
Thomas Cheatham
Re: [AMBER] What is the most modern AMBER parm/top format?
(Fri Jan 22 2016 - 09:23:30 PST)
Tom Kurtzman
Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15
(Sat Jan 23 2016 - 05:47:09 PST)
Vasantha Kumar
Re: [AMBER] atom clash and close contact after MD simulation in water
(Wed Jan 27 2016 - 08:48:44 PST)
Re: [AMBER] atom clash and close contact after MD simulation in water
(Wed Jan 27 2016 - 08:40:14 PST)
[AMBER] atom clash and close contact after MD simulation in water
(Wed Jan 27 2016 - 05:50:41 PST)
Re: [AMBER] RMSD w.r.t reference structure
(Wed Jan 27 2016 - 03:21:53 PST)
Re: [AMBER] How to put ACE and NME on the ends of a missing loop
(Fri Jan 22 2016 - 06:37:36 PST)
Re: [AMBER] python error when using pdb4amber
(Tue Jan 19 2016 - 05:29:19 PST)
Vertika Gautam
Re: [AMBER] RMSD selected residues
(Fri Jan 15 2016 - 23:52:18 PST)
[AMBER] RMSD selected residues
(Tue Jan 12 2016 - 23:02:58 PST)
Vu Truong
[AMBER] Questions about Steered MD in Amber
(Thu Jan 14 2016 - 12:10:59 PST)
[AMBER] Questions about Steered MD in Amber
(Fri Jan 08 2016 - 15:23:36 PST)
Wong Li Zhe
[AMBER] Error Message
(Thu Jan 28 2016 - 19:07:41 PST)
Re: [AMBER] Kinetic Energy
(Wed Jan 13 2016 - 18:09:43 PST)
Re: [AMBER] Kinetic Energy
(Wed Jan 13 2016 - 17:25:13 PST)
[AMBER] Kinetic Energy
(Wed Jan 13 2016 - 15:54:50 PST)
[AMBER] Xmgrace
(Mon Jan 11 2016 - 18:26:54 PST)
wyq
Re: [AMBER] Errors during Building Sidechain Model（MCPB program）
(Fri Jan 08 2016 - 03:44:06 PST)
Yin, Guowei
Re: [AMBER] parameters for Mono-methylated Lysine
(Tue Jan 12 2016 - 11:13:09 PST)
Yogeeshwar Ajjugal
[AMBER] Error in running AMBER 12 GPU simulations[application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0]
(Wed Jan 06 2016 - 21:43:47 PST)
zengxitao
[AMBER] QM/MM/MD simulation
(Fri Jan 15 2016 - 05:49:17 PST)
יוכבד
Re: [AMBER] Amber14 Installation with cuda
(Thu Jan 21 2016 - 10:31:13 PST)
[AMBER] Amber14 Installation with cuda
(Thu Jan 21 2016 - 06:30:12 PST)
王远强
Re: [AMBER] Errors during Building Sidechain Model（MCPB program）
(Wed Jan 06 2016 - 20:58:26 PST)
[AMBER] Errors during Building Sidechain Model（MCPB program）
(Wed Jan 06 2016 - 20:38:31 PST)
Last message date
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Fri Jan 29 2016 - 15:00:03 PST
Archived on
: Sun Nov 24 2024 - 05:55:30 PST
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