Amber Archive Mar 2017 by author
468 messages
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Starting
Wed Mar 01 2017 - 00:00:03 PST,
Ending
Fri Mar 31 2017 - 16:30:03 PDT
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abdennour braka
[AMBER] Question about the implementation of the Steered MD
(Thu Mar 09 2017 - 23:26:36 PST)
ABEL Stephane
Re: [AMBER] dUMP parameters
(Sun Mar 05 2017 - 09:03:19 PST)
Abhilash J
Re: [AMBER] DU issue with Antechamber
(Thu Mar 30 2017 - 03:21:14 PDT)
Re: [AMBER] DU issue with Antechamber
(Sat Mar 25 2017 - 00:16:26 PDT)
[AMBER] DU issue with Antechamber
(Wed Mar 22 2017 - 21:21:37 PDT)
Re: [AMBER] Error in Cobalt parameters in CO-METHYLCOBALAMIN with MCPB.py
(Wed Mar 15 2017 - 04:42:47 PDT)
[AMBER] Error in Cobalt parameters in CO-METHYLCOBALAMIN with MCPB.py
(Wed Mar 08 2017 - 01:45:50 PST)
Re: [AMBER] prepare prepin file from MCPB results
(Wed Mar 08 2017 - 01:31:34 PST)
[AMBER] prepare prepin file from MCPB results
(Mon Mar 06 2017 - 00:34:14 PST)
Adrian Roitberg
Re: [AMBER] Question about the propagation of error in MM/PBSA binding free energy calculation.
(Tue Mar 28 2017 - 10:11:17 PDT)
Re: [AMBER] Force/Energy vs extension curve from Steered MD
(Sat Mar 25 2017 - 11:31:03 PDT)
Re: [AMBER] Force/Energy vs extension curve from Steered MD
(Sat Mar 25 2017 - 11:03:39 PDT)
Re: [AMBER] 来自zengxitao的邮件
(Wed Mar 22 2017 - 10:30:23 PDT)
Re: [AMBER] CpHMD: how is the charged system treated?
(Wed Mar 22 2017 - 07:18:23 PDT)
[AMBER] timerge question
(Thu Mar 16 2017 - 07:48:09 PDT)
Re: [AMBER] error explicit solvent CpHMD production run
(Wed Mar 08 2017 - 07:30:21 PST)
Re: [AMBER] error explicit solvent CpHMD production run
(Tue Mar 07 2017 - 05:25:14 PST)
Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds
(Fri Mar 03 2017 - 07:02:52 PST)
Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds
(Fri Mar 03 2017 - 06:51:50 PST)
Aishani Prem
[AMBER] Error: FATAL: Atom .R<ZN 2>.A<ZN 1> does not have a type.
(Tue Mar 28 2017 - 18:22:06 PDT)
Alice Zeng
[AMBER] How to use MCPB.py to generate OH parameters
(Sun Mar 12 2017 - 21:25:36 PDT)
Alicia Merlino
Re: [AMBER] problems with heating
(Mon Mar 06 2017 - 20:44:37 PST)
Amy Rice
Re: [AMBER] Generate psf file for chamber
(Thu Mar 09 2017 - 09:04:04 PST)
Andreas Tosstorff
Re: [AMBER] Water molecules show three bonds in VMD
(Thu Mar 30 2017 - 04:20:20 PDT)
[AMBER] Dimer trajectory analysis
(Wed Mar 29 2017 - 09:34:23 PDT)
Re: [AMBER] FEW- issues generating parameter files for MD
(Wed Mar 29 2017 - 00:50:05 PDT)
Re: [AMBER] Split a Large trajectory into smaller trajectory
(Wed Mar 29 2017 - 00:38:14 PDT)
Re: [AMBER] FEW- issues generating parameter files for MD
(Tue Mar 28 2017 - 08:45:41 PDT)
Re: [AMBER] FEW- issues generating parameter files for MD
(Tue Mar 28 2017 - 07:24:31 PDT)
Re: [AMBER] FEW- issues generating parameter files for MD
(Mon Mar 27 2017 - 08:28:06 PDT)
Re: [AMBER] surf cpptraj non-standard residue
(Mon Mar 27 2017 - 07:56:27 PDT)
Re: [AMBER] FEW- issues generating parameter files for MD
(Mon Mar 27 2017 - 07:20:53 PDT)
Re: [AMBER] surf cpptraj non-standard residue
(Mon Mar 27 2017 - 05:50:18 PDT)
[AMBER] surf cpptraj non-standard residue
(Mon Mar 27 2017 - 05:29:01 PDT)
Re: [AMBER] Problem with keyboard in xleap
(Wed Mar 22 2017 - 04:33:18 PDT)
Re: [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered
(Thu Mar 09 2017 - 02:29:59 PST)
[AMBER] REMD processor number
(Thu Mar 02 2017 - 09:04:47 PST)
Andrew Schaub
Re: [AMBER] Error: FATAL: Atom .R<ZN 2>.A<ZN 1> does not have a type.
(Tue Mar 28 2017 - 20:47:47 PDT)
Re: [AMBER] Antechamber Error
(Sat Mar 25 2017 - 00:30:38 PDT)
Arnoult, Eric [JRDUS]
[AMBER] AWS GPU node crashes with AMBER 16
(Wed Mar 22 2017 - 10:35:11 PDT)
Atila Petrosian
[AMBER] 1-4 VDW and 1-4 EEL Energy Components in mm-gbsa
(Fri Mar 03 2017 - 01:01:24 PST)
Baker, Joseph
Re: [AMBER] autoimage for a protein filament
(Thu Mar 30 2017 - 10:44:22 PDT)
[AMBER] autoimage for a protein filament
(Wed Mar 29 2017 - 19:10:08 PDT)
Beale, John
Re: [AMBER] Accelerated MD
(Thu Mar 09 2017 - 04:49:36 PST)
Re: [AMBER] Accelerated MD
(Thu Mar 09 2017 - 04:47:56 PST)
[AMBER] Accelerated MD
(Thu Mar 09 2017 - 02:51:12 PST)
Bharatham, Nagakumar
[AMBER] Fw: MM/GBSA residual decomposition issue
(Fri Mar 17 2017 - 07:50:48 PDT)
[AMBER] MM/GBSA residual decomposition issue
(Fri Mar 17 2017 - 05:29:57 PDT)
Bill Ross
Re: [AMBER] Dimer trajectory analysis
(Wed Mar 29 2017 - 09:41:22 PDT)
Re: [AMBER] Why molecular dynamics simulation was stopped without giving any error
(Thu Mar 23 2017 - 00:42:16 PDT)
Re: [AMBER] Difficulty using noshakemask in Amber15
(Tue Mar 21 2017 - 16:49:00 PDT)
Re: [AMBER] unable to solvate a polymer
(Tue Mar 21 2017 - 16:12:29 PDT)
Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit
(Sat Mar 18 2017 - 22:46:07 PDT)
Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit
(Fri Mar 17 2017 - 23:55:50 PDT)
Re: [AMBER] Issues running TI simulations
(Thu Mar 16 2017 - 02:36:50 PDT)
Re: [AMBER] Issues running TI simulations
(Thu Mar 16 2017 - 02:24:42 PDT)
Re: [AMBER] Installing AmberTools16 - Sierra MacOs
(Mon Mar 13 2017 - 14:30:10 PDT)
Re: [AMBER] Installing AmberTools16 - Sierra MacOs
(Mon Mar 13 2017 - 14:02:44 PDT)
Re: [AMBER] Query regarding extension of Molecular dynamics simulation from 50ns to 100ns
(Mon Mar 06 2017 - 21:09:10 PST)
Bruno Falcone
Re: [AMBER] Issue regarding ligand parameterization
(Mon Mar 20 2017 - 07:21:22 PDT)
Re: [AMBER] MM energy contributions of atoms in a molecule
(Wed Mar 01 2017 - 06:43:33 PST)
Budhathoki, Dipesh
Re: [AMBER] RE : suitable basis sets for QM/MM
(Thu Mar 16 2017 - 13:51:04 PDT)
[AMBER] RE : suitable basis sets for QM/MM
(Thu Mar 16 2017 - 10:49:00 PDT)
Charles Lin
Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16
(Thu Mar 30 2017 - 12:26:04 PDT)
Chase Zagorec-Marks
Re: [AMBER] Difficulty using noshakemask in Amber15
(Wed Mar 22 2017 - 10:16:25 PDT)
[AMBER] Difficulty using noshakemask in Amber15
(Tue Mar 21 2017 - 16:43:03 PDT)
Chitrak Gupta
[AMBER] Restraint on Z-projection of a distance
(Fri Mar 24 2017 - 11:44:53 PDT)
Chris Neale
Re: [AMBER] restarting Amber calculations gives abnormal structures
(Fri Mar 31 2017 - 10:01:10 PDT)
Re: [AMBER] restarting Amber calculations gives abnormal structures
(Fri Mar 31 2017 - 09:30:34 PDT)
Re: [AMBER] restarting Amber calculations gives abnormal structures
(Wed Mar 29 2017 - 12:36:15 PDT)
Re: [AMBER] what hardware is required for gou peer-ro-peer an how imporant is gpu-to-gpu nvlink
(Tue Mar 28 2017 - 22:07:13 PDT)
Re: [AMBER] what hardware is required for gou peer-ro-peer an how imporant is gpu-to-gpu nvlink
(Tue Mar 28 2017 - 19:27:43 PDT)
[AMBER] what hardware is required for gou peer-ro-peer an how imporant is gpu-to-gpu nvlink
(Tue Mar 28 2017 - 17:38:22 PDT)
Daniel Mermelstein
Re: [AMBER] timerge question
(Thu Mar 16 2017 - 15:47:31 PDT)
Daniel Roe
Re: [AMBER] restarting Amber calculations gives abnormal structures
(Fri Mar 31 2017 - 09:57:01 PDT)
Re: [AMBER] coordinates in restraint mast
(Fri Mar 31 2017 - 09:24:20 PDT)
Re: [AMBER] coordinates in restraint mast
(Fri Mar 31 2017 - 08:14:53 PDT)
Re: [AMBER] Water molecules show three bonds in VMD
(Thu Mar 30 2017 - 05:23:00 PDT)
Re: [AMBER] autoimage for a protein filament
(Thu Mar 30 2017 - 05:20:20 PDT)
Re: [AMBER] Dimer trajectory analysis
(Thu Mar 30 2017 - 05:16:58 PDT)
Re: [AMBER] Cpptraj problems
(Thu Mar 30 2017 - 05:03:10 PDT)
Re: [AMBER] RDF plot
(Tue Mar 28 2017 - 10:49:46 PDT)
Re: [AMBER] RDF plot
(Tue Mar 28 2017 - 10:16:47 PDT)
Re: [AMBER] RDF plot
(Tue Mar 28 2017 - 09:55:37 PDT)
Re: [AMBER] RDF plot
(Tue Mar 28 2017 - 06:59:32 PDT)
Re: [AMBER] Linkage problem in branched oligosaccharide
(Tue Mar 28 2017 - 06:22:22 PDT)
Re: [AMBER] water bridge
(Tue Mar 28 2017 - 06:20:22 PDT)
Re: [AMBER] surf cpptraj non-standard residue
(Mon Mar 27 2017 - 08:02:25 PDT)
Re: [AMBER] Installation issue
(Sat Mar 25 2017 - 05:59:51 PDT)
Re: [AMBER] renumber residues
(Fri Mar 24 2017 - 08:01:16 PDT)
Re: [AMBER] cpptraj distance between centroid of a ring and an atom
(Thu Mar 23 2017 - 05:11:36 PDT)
Re: [AMBER] Is it possible to create a bugreport.ambermd.org mailinglist?
(Wed Mar 22 2017 - 06:04:30 PDT)
Re: [AMBER] Problem with keyboard in xleap
(Wed Mar 22 2017 - 05:38:21 PDT)
Re: [AMBER] Select specific frames within cpptraj?
(Tue Mar 21 2017 - 13:17:37 PDT)
Re: [AMBER] help in RDF
(Tue Mar 21 2017 - 08:30:33 PDT)
Re: [AMBER] pmemd.MPI error on lonestar5 super comp.
(Mon Mar 20 2017 - 05:30:49 PDT)
Re: [AMBER] 2D rms plot doubt
(Mon Mar 20 2017 - 05:27:20 PDT)
Re: [AMBER] 2D rms plot doubt
(Mon Mar 20 2017 - 05:23:33 PDT)
Re: [AMBER] 2D rms plot doubt
(Sat Mar 18 2017 - 09:36:55 PDT)
Re: [AMBER] converting trajectory file from NAMD to AMBER
(Thu Mar 16 2017 - 08:05:45 PDT)
Re: [AMBER] distance calculations - Protein-RNA
(Thu Mar 16 2017 - 05:41:05 PDT)
Re: [AMBER] About PCA with cpptraj
(Wed Mar 15 2017 - 10:03:19 PDT)
Re: [AMBER] Help with reconstructing pH-based mdcrd (trajectory) files
(Wed Mar 15 2017 - 07:17:10 PDT)
Re: [AMBER] Help with reconstructing pH-based mdcrd (trajectory) files
(Wed Mar 15 2017 - 06:15:05 PDT)
Re: [AMBER] Installing AmberTools16 - ld library issue
(Mon Mar 13 2017 - 10:37:58 PDT)
Re: [AMBER] Problem in configuring+compiling cpptraj development version with Sander compiled with AmberTools16
(Fri Mar 10 2017 - 05:38:59 PST)
Re: [AMBER] Problem in configuring+compiling cpptraj development version with Sander compiled with AmberTools16
(Fri Mar 10 2017 - 05:05:24 PST)
Re: [AMBER] AmberTools compilation
(Thu Mar 09 2017 - 06:08:32 PST)
Re: [AMBER] AmberTools compilation
(Thu Mar 09 2017 - 05:48:02 PST)
Re: [AMBER] Accelerated MD
(Thu Mar 09 2017 - 05:36:51 PST)
Re: [AMBER] AmberTools compilation
(Thu Mar 09 2017 - 05:33:00 PST)
Re: [AMBER] rdf_with_center_in_cpptraj_16
(Mon Mar 06 2017 - 05:21:05 PST)
Re: [AMBER] How to make rst file by using ptraj
(Sun Mar 05 2017 - 04:40:32 PST)
Re: [AMBER] How to make rst file by using ptraj
(Sat Mar 04 2017 - 12:19:13 PST)
Re: [AMBER] When does cpptraj use information from the original pdb file?
(Fri Mar 03 2017 - 07:02:11 PST)
Re: [AMBER] cpptraj: dihcovar and projection need trajin to work properly?
(Wed Mar 01 2017 - 10:01:44 PST)
Re: [AMBER] cpptraj: dihcovar and projection need trajin to work properly?
(Wed Mar 01 2017 - 08:26:10 PST)
Re: [AMBER] Holes/bubbles in water during NVT (fix atoms)
(Wed Mar 01 2017 - 08:17:51 PST)
Re: [AMBER] Methods to count the different species
(Wed Mar 01 2017 - 08:13:56 PST)
David Case
Re: [AMBER] restarting Amber calculations gives abnormal structures
(Fri Mar 31 2017 - 11:18:31 PDT)
Re: [AMBER] Linkage problem in branched oligosaccharide
(Wed Mar 29 2017 - 04:57:40 PDT)
Re: [AMBER] restarting Amber calculations gives abnormal structures
(Wed Mar 29 2017 - 04:50:28 PDT)
Re: [AMBER] DU issue with Antechamber
(Tue Mar 28 2017 - 10:01:36 PDT)
Re: [AMBER] restarting Amber calculations gives abnormal structures
(Tue Mar 28 2017 - 09:47:13 PDT)
Re: [AMBER-Developers] web site inaccessible?
(Mon Mar 27 2017 - 07:31:14 PDT)
Re: [AMBER] Antechamber Error
(Sat Mar 25 2017 - 08:21:09 PDT)
Re: [AMBER] renumber residues
(Fri Mar 24 2017 - 11:05:59 PDT)
Re: [AMBER] How to perform Newton-Raphson minimization to protein
(Fri Mar 24 2017 - 07:20:28 PDT)
Re: [AMBER] 发自刘兰茹的邮件
(Fri Mar 24 2017 - 05:19:58 PDT)
Re: [AMBER] How to perform Newton-Raphson minimization to protein
(Thu Mar 23 2017 - 06:38:01 PDT)
Re: [AMBER] Why molecular dynamics simulation was stopped without giving any error
(Thu Mar 23 2017 - 06:36:02 PDT)
Re: [AMBER] DU issue with Antechamber
(Thu Mar 23 2017 - 06:32:47 PDT)
Re: [AMBER] Problem with keyboard in xleap
(Wed Mar 22 2017 - 08:40:36 PDT)
Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16?
(Wed Mar 22 2017 - 08:24:20 PDT)
Re: [AMBER] unable to solvate a polymer
(Wed Mar 22 2017 - 08:18:00 PDT)
Re: [AMBER] Nmode using MMPBSA.py
(Wed Mar 22 2017 - 08:12:42 PDT)
Re: [AMBER] Problems in using Parmchk2
(Tue Mar 21 2017 - 07:15:51 PDT)
Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16?
(Mon Mar 20 2017 - 07:44:01 PDT)
Re: [AMBER] Issue regarding ligand parameterization
(Mon Mar 20 2017 - 05:06:17 PDT)
Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit
(Sat Mar 18 2017 - 08:22:33 PDT)
Re: [AMBER] How to generate inputfile
(Fri Mar 17 2017 - 07:12:57 PDT)
Re: [AMBER] How to generate inputfile
(Thu Mar 16 2017 - 05:54:26 PDT)
Re: [AMBER] Problems in using Parmchk2
(Thu Mar 16 2017 - 05:50:56 PDT)
Re: [AMBER] Problems in using Parmchk2
(Wed Mar 15 2017 - 15:10:50 PDT)
Re: [AMBER] How to generate inputfile
(Wed Mar 15 2017 - 07:19:25 PDT)
Re: [AMBER] prepc vs prepi
(Tue Mar 14 2017 - 14:43:28 PDT)
Re: [AMBER] problem with solvation
(Tue Mar 14 2017 - 07:27:52 PDT)
Re: [AMBER] A problem about the frcmod produced by ParmChk
(Mon Mar 13 2017 - 19:15:23 PDT)
Re: [AMBER] Unperturbed charge of the unit is not zero
(Mon Mar 13 2017 - 19:03:40 PDT)
Re: [AMBER] Error for reading the amber rst file
(Mon Mar 13 2017 - 08:02:23 PDT)
Re: [AMBER] Simulating a protein with modified amino acid residue, the saga continues. Atom ... does not have a type.
(Fri Mar 10 2017 - 11:13:03 PST)
Re: [AMBER] Boron's parameter
(Fri Mar 10 2017 - 07:27:07 PST)
Re: [AMBER] anionic Ser ?
(Thu Mar 09 2017 - 06:21:12 PST)
Re: [AMBER] AmberTools compilation
(Thu Mar 09 2017 - 06:16:50 PST)
Re: [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered
(Thu Mar 09 2017 - 05:07:12 PST)
Re: [AMBER] OPEN SHELL MOLECULES
(Wed Mar 08 2017 - 18:57:47 PST)
Re: [AMBER] problems with heating
(Tue Mar 07 2017 - 05:04:43 PST)
Re: [AMBER] Amber 16 MD simulation Problems
(Mon Mar 06 2017 - 18:39:03 PST)
Re: [AMBER] Simulating a protein with modified amino acid residue, the saga continues. Atom ... does not have a type.
(Mon Mar 06 2017 - 18:36:03 PST)
Re: [AMBER] Amber 16 MD simulation Problems
(Sun Mar 05 2017 - 10:21:47 PST)
Re: [AMBER] dUMP parameters
(Sun Mar 05 2017 - 10:17:09 PST)
Re: [AMBER] How to make rst file by using ptraj
(Sat Mar 04 2017 - 12:51:02 PST)
David Cerutti
Re: [AMBER] Holes/bubbles in water during NVT (fix atoms)
(Wed Mar 01 2017 - 02:33:00 PST)
David Poole
Re: [AMBER] How to generate inputfile (???)
(Thu Mar 16 2017 - 12:08:50 PDT)
Diego Gomes
[AMBER] pmemd.cuda and taskset on K80
(Wed Mar 01 2017 - 08:10:24 PST)
diego.soler.uam.es
[AMBER] Generate DNA sequence with a mismatch
(Fri Mar 17 2017 - 04:39:43 PDT)
Dwight McGee
Re: [AMBER] Nmode using MMPBSA.py
(Wed Mar 22 2017 - 09:29:52 PDT)
EGIDEA PUTI DEVINA
Re: [AMBER] error explicit solvent CpHMD production run
(Wed Mar 08 2017 - 01:41:11 PST)
[AMBER] error explicit solvent CpHMD production run
(Mon Mar 06 2017 - 22:05:05 PST)
Elisa Pieri
[AMBER] CpHMD: how is the charged system treated?
(Wed Mar 22 2017 - 06:33:30 PDT)
[AMBER] Potential on QM atoms - details about cutoff
(Fri Mar 10 2017 - 07:13:19 PST)
Elvis Martis
Re: [AMBER] Error: FATAL: Atom .R<ZN 2>.A<ZN 1> does not have a type.
(Tue Mar 28 2017 - 21:28:23 PDT)
Re: [AMBER] surf cpptraj non-standard residue
(Mon Mar 27 2017 - 06:24:50 PDT)
Re: [AMBER] surf cpptraj non-standard residue
(Mon Mar 27 2017 - 05:38:39 PDT)
Re: [AMBER] Antechamber Error
(Thu Mar 23 2017 - 02:59:26 PDT)
Re: [AMBER] Antechamber Error
(Thu Mar 23 2017 - 01:58:53 PDT)
Re: [AMBER] Problem with keyboard in xleap
(Wed Mar 22 2017 - 05:23:41 PDT)
Re: [AMBER] Antechamber Error
(Tue Mar 21 2017 - 00:15:27 PDT)
Re: [AMBER] 2D rms plot doubt
(Sat Mar 18 2017 - 03:11:19 PDT)
Re: [AMBER] converting trajectory file from NAMD to AMBER
(Thu Mar 16 2017 - 09:37:06 PDT)
Re: [AMBER] converting trajectory file from NAMD to AMBER
(Thu Mar 16 2017 - 07:45:43 PDT)
Re: [AMBER] Generating topology from Gaussian 09
(Thu Mar 16 2017 - 07:25:26 PDT)
Re: [AMBER] About PCA with cpptraj
(Wed Mar 15 2017 - 10:06:26 PDT)
[AMBER] About PCA with cpptraj
(Wed Mar 15 2017 - 09:34:00 PDT)
Re: [AMBER] Intel Xeon Phi 7120P
(Wed Mar 15 2017 - 00:03:44 PDT)
Re: [AMBER] Query regarding extension of Molecular dynamics simulation from 50ns to 100ns
(Mon Mar 06 2017 - 21:07:32 PST)
Re: [AMBER] Query regarding extension of Molecular dynamics simulation from 50ns to 100ns
(Mon Mar 06 2017 - 21:04:21 PST)
Re: [AMBER] Query regarding extension of Molecular dynamics simulation from 50ns to 100ns
(Mon Mar 06 2017 - 20:35:14 PST)
Re: [AMBER] Amber 16 MD simulation Problems
(Mon Mar 06 2017 - 03:22:26 PST)
Re: [AMBER] prepare prepin file from MCPB results
(Mon Mar 06 2017 - 02:38:50 PST)
Re: [AMBER] dUMP parameters
(Sun Mar 05 2017 - 07:58:29 PST)
Re: [AMBER] dUMP parameters
(Sun Mar 05 2017 - 07:37:07 PST)
Re: [AMBER] dUMP parameters
(Sun Mar 05 2017 - 07:34:01 PST)
Re: [AMBER] Amber 16 MD simulation Problems
(Sun Mar 05 2017 - 02:28:54 PST)
Eric Lang
Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds
(Wed Mar 15 2017 - 01:49:03 PDT)
Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds
(Tue Mar 14 2017 - 07:40:22 PDT)
Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds
(Fri Mar 03 2017 - 07:01:36 PST)
Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds
(Fri Mar 03 2017 - 06:52:38 PST)
Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds
(Fri Mar 03 2017 - 06:33:24 PST)
Erma Fatiha Muhammad
[AMBER] Installing Amber14 and AmberTools15 Error
(Wed Mar 29 2017 - 19:59:11 PDT)
Eugene Cha
[AMBER] Unperturbed charge of the unit is not zero
(Mon Mar 13 2017 - 07:09:29 PDT)
Feng Pan
Re: [AMBER] Restraint on Z-projection of a distance
(Fri Mar 24 2017 - 12:15:50 PDT)
Re: [AMBER] Question about the implementation of the Steered MD
(Fri Mar 10 2017 - 08:45:31 PST)
FyD
Re: [AMBER] Simulating a protein with modified amino acid residue, the saga continues. Atom ... does not have a type.
(Fri Mar 10 2017 - 09:30:22 PST)
Re: [AMBER] anionic Ser ?
(Fri Mar 10 2017 - 06:08:38 PST)
Re: [AMBER] Simulating a protein with modified amino acid residue, the saga continues. Atom ... does not have a type.
(Tue Mar 07 2017 - 01:30:34 PST)
Re: [AMBER] dUMP parameters
(Mon Mar 06 2017 - 22:57:11 PST)
Garima Singh
[AMBER] Why molecular dynamics simulation was stopped without giving any error
(Wed Mar 22 2017 - 23:36:01 PDT)
George Tzotzos
[AMBER] Amber Mailing List problem
(Thu Mar 30 2017 - 06:59:43 PDT)
[AMBER] Preparation of ligand enantiomers
(Tue Mar 28 2017 - 10:14:45 PDT)
[AMBER] Installation issue
(Sat Mar 25 2017 - 05:37:03 PDT)
Giannis Gl
Re: [AMBER] Installing AmberTools16 - Sierra MacOs
(Mon Mar 13 2017 - 14:08:14 PDT)
Re: [AMBER] Installing AmberTools16 - Sierra MacOs
(Mon Mar 13 2017 - 14:01:56 PDT)
Re: [AMBER] Installing AmberTools16 - Sierra MacOs
(Mon Mar 13 2017 - 14:00:24 PDT)
Re: [AMBER] Installing AmberTools16 - Sierra MacOs
(Mon Mar 13 2017 - 13:46:28 PDT)
Re: [AMBER] Installing AmberTools16 - Sierra MacOs
(Mon Mar 13 2017 - 13:32:11 PDT)
[AMBER] Installing AmberTools16 - Sierra MacOs
(Mon Mar 13 2017 - 12:10:49 PDT)
Re: [AMBER] Installing AmberTools16 - ld library issue
(Mon Mar 13 2017 - 11:14:52 PDT)
[AMBER] Installing AmberTools16 - ld library issue
(Mon Mar 13 2017 - 10:32:43 PDT)
giulia palermo
[AMBER] Fwd: H-bonds matrix
(Thu Mar 02 2017 - 11:59:33 PST)
[AMBER] H-bonds matrix
(Thu Mar 02 2017 - 09:26:11 PST)
Goetz, Andreas
Re: [AMBER] RE : suitable basis sets for QM/MM
(Thu Mar 16 2017 - 12:25:00 PDT)
Re: [AMBER] Error when running QM/MM MD for actinide and lanthanide system by amber
(Mon Mar 13 2017 - 20:30:27 PDT)
Gustavo Seabra
Re: [AMBER] RDF plot
(Tue Mar 28 2017 - 05:55:07 PDT)
Re: [AMBER] RDF plot
(Tue Mar 28 2017 - 04:26:15 PDT)
Hai Nguyen
Re: [AMBER] Issues Regaring the PDB files from Trajectory frames
(Fri Mar 31 2017 - 14:37:45 PDT)
Re: [AMBER] Issues Regaring the PDB files from Trajectory frames
(Fri Mar 31 2017 - 14:27:14 PDT)
Re: [AMBER-Developers] web site inaccessible?
(Mon Mar 27 2017 - 07:54:20 PDT)
Re: [AMBER] Error Importing pytraj to Python 2.7 Program
(Tue Mar 21 2017 - 14:59:53 PDT)
Re: [AMBER] Error Importing pytraj to Python 2.7 Program
(Tue Mar 21 2017 - 14:35:38 PDT)
Re: [AMBER] Is it possible to create a bugreport.ambermd.org mailinglist?
(Tue Mar 21 2017 - 13:23:07 PDT)
Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit
(Mon Mar 20 2017 - 08:46:30 PDT)
Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit
(Sat Mar 18 2017 - 23:19:36 PDT)
Re: [AMBER] C/Fortran compilation
(Fri Mar 17 2017 - 09:00:15 PDT)
Re: [AMBER] Fw: MM/GBSA residual decomposition issue
(Fri Mar 17 2017 - 08:13:18 PDT)
Re: [AMBER] converting trajectory file from NAMD to AMBER
(Thu Mar 16 2017 - 09:49:09 PDT)
Re: [AMBER] How to get parmed.py script?
(Wed Mar 15 2017 - 06:11:40 PDT)
Re: [AMBER] Installing AmberTools16 - Sierra MacOs
(Mon Mar 13 2017 - 14:23:25 PDT)
Re: [AMBER] Installing AmberTools16 - Sierra MacOs
(Mon Mar 13 2017 - 14:11:56 PDT)
Re: [AMBER] Installing AmberTools16 - Sierra MacOs
(Mon Mar 13 2017 - 13:57:06 PDT)
Re: [AMBER] Installing AmberTools16 - Sierra MacOs
(Mon Mar 13 2017 - 13:51:56 PDT)
Re: [AMBER] Installing AmberTools16 - Sierra MacOs
(Mon Mar 13 2017 - 13:37:37 PDT)
Re: [AMBER] Installing AmberTools16 - Sierra MacOs
(Mon Mar 13 2017 - 13:27:50 PDT)
Re: [AMBER] Installing AmberTools16 - Sierra MacOs
(Mon Mar 13 2017 - 13:27:09 PDT)
Re: [AMBER] Installing AmberTools16 - ld library issue
(Mon Mar 13 2017 - 11:03:14 PDT)
Re: [AMBER] Memory footprint goes on increasing: pytraj traj.iterchunk used, distances between bonds calculation
(Sun Mar 12 2017 - 14:34:49 PDT)
Re: [AMBER] Memory footprint goes on increasing: pytraj traj.iterchunk used, distances between bonds calculation
(Sun Mar 12 2017 - 14:30:15 PDT)
Re: [AMBER] Problem in configuring+compiling cpptraj development version with Sander compiled with AmberTools16
(Fri Mar 10 2017 - 07:26:32 PST)
Re: [AMBER] AmberTools compilation
(Thu Mar 09 2017 - 07:40:25 PST)
Re: [AMBER] AmberTools compilation
(Thu Mar 09 2017 - 07:30:23 PST)
Re: [AMBER] AmberTools compilation
(Thu Mar 09 2017 - 07:23:15 PST)
Re: [AMBER] OPEN SHELL MOLECULES
(Wed Mar 08 2017 - 14:38:30 PST)
Hannes Loeffler
Re: [AMBER] coordinates in restraint mast
(Fri Mar 31 2017 - 06:35:34 PDT)
Re: [AMBER] Thermodynamic integration simulations issues
(Tue Mar 28 2017 - 06:21:26 PDT)
Re: [AMBER] Questions about Amber TI tutorial
(Wed Mar 22 2017 - 01:19:25 PDT)
Re: [AMBER] Questions about Amber TI tutorial
(Tue Mar 21 2017 - 13:56:48 PDT)
Re: [AMBER] timerge question
(Fri Mar 17 2017 - 02:38:06 PDT)
Re: [AMBER] how to use TImerge to do TI simulations
(Tue Mar 07 2017 - 07:25:51 PST)
Re: [AMBER] reg "rel delta G binding computation using TIMD"
(Mon Mar 06 2017 - 03:43:40 PST)
Ingvild Isaksen
Re: [AMBER] Help with reconstructing pH-based mdcrd (trajectory) files
(Wed Mar 15 2017 - 07:26:26 PDT)
Re: [AMBER] Help with reconstructing pH-based mdcrd (trajectory) files
(Wed Mar 15 2017 - 06:42:21 PDT)
[AMBER] Help with reconstructing pH-based mdcrd (trajectory) files
(Wed Mar 15 2017 - 05:13:32 PDT)
Jason Swails
Re: [AMBER] what hardware is required for gou peer-ro-peer an how imporant is gpu-to-gpu nvlink
(Tue Mar 28 2017 - 21:27:13 PDT)
Re: [AMBER] what hardware is required for gou peer-ro-peer an how imporant is gpu-to-gpu nvlink
(Tue Mar 28 2017 - 21:19:54 PDT)
Re: [AMBER] what hardware is required for gou peer-ro-peer an how imporant is gpu-to-gpu nvlink
(Tue Mar 28 2017 - 19:09:22 PDT)
Re: [AMBER] Force/Energy vs extension curve from Steered MD
(Sun Mar 26 2017 - 17:27:26 PDT)
Re: [AMBER] Chamber error; No NONBONDED
(Thu Mar 23 2017 - 20:22:38 PDT)
Re: [AMBER] install AMBER16 GTX480
(Mon Mar 20 2017 - 11:29:30 PDT)
Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16?
(Mon Mar 20 2017 - 11:24:28 PDT)
Re: [AMBER] timerge question
(Sat Mar 18 2017 - 11:33:10 PDT)
Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds
(Tue Mar 14 2017 - 10:53:25 PDT)
Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds
(Fri Mar 03 2017 - 06:47:53 PST)
Re: [AMBER] 1-4 VDW and 1-4 EEL Energy Components in mm-gbsa
(Fri Mar 03 2017 - 06:09:00 PST)
jinfeng liu
[AMBER] Boron's parameter
(Fri Mar 10 2017 - 04:35:54 PST)
JinpengYang
[AMBER] A problem about the frcmod produced by ParmChk
(Mon Mar 13 2017 - 18:07:16 PDT)
Jon Mujika
[AMBER] unable to solvate a polymer
(Tue Mar 21 2017 - 16:00:19 PDT)
Junmei Wang
Re: [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue
(Thu Mar 02 2017 - 08:13:04 PST)
Kanin Wichapong
[AMBER] install AMBER16 GTX480
(Mon Mar 20 2017 - 06:46:54 PDT)
[AMBER] C/Fortran compilation
(Fri Mar 17 2017 - 08:42:27 PDT)
Karl Kirschner
Re: [AMBER] How to get parmed.py script?
(Wed Mar 15 2017 - 03:25:13 PDT)
Kat G
[AMBER] constraint residues while enhanced sampling simulation
(Wed Mar 29 2017 - 13:40:43 PDT)
Kenneth Huang
[AMBER] Select specific frames within cpptraj?
(Tue Mar 21 2017 - 13:03:03 PDT)
konda003 .
Re: [AMBER] Nmode using MMPBSA.py
(Tue Mar 21 2017 - 14:06:36 PDT)
[AMBER] NMODE ERROR MESSAGE
(Fri Mar 17 2017 - 09:02:46 PDT)
[AMBER] Distance between benzene ring of one molecule and centre of mass of other molecule
(Wed Mar 01 2017 - 13:54:53 PST)
Kshatresh Dutta Dubey
[AMBER] Application of external electric field with QM/MM in Amber
(Tue Mar 07 2017 - 12:47:15 PST)
kungking Hanpaibool
[AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered
(Thu Mar 09 2017 - 01:59:04 PST)
Lachele Foley
Re: [AMBER] Linkage problem in branched oligosaccharide
(Thu Mar 30 2017 - 05:39:52 PDT)
liulr13.mails.jlu.edu.cn
Re: [AMBER] 发自刘兰茹的邮件
(Fri Mar 24 2017 - 02:30:36 PDT)
Liyang Zhu
Re: [AMBER] Methods to count the different species
(Wed Mar 01 2017 - 18:24:39 PST)
Lovika Mittal
Re: [AMBER] Query regarding extension of Molecular dynamics simulation from 50ns to 100ns
(Mon Mar 06 2017 - 20:59:15 PST)
[AMBER] Query regarding extension of Molecular dynamics simulation from 50ns to 100ns
(Mon Mar 06 2017 - 20:26:12 PST)
luca maggi
Re: [AMBER] Antechamber Error
(Thu Mar 23 2017 - 02:28:17 PDT)
Re: [AMBER] Antechamber Error
(Thu Mar 23 2017 - 00:09:58 PDT)
[AMBER] Antechamber Error
(Mon Mar 20 2017 - 23:56:51 PDT)
Manju Sah
Re: [AMBER] Linkage problem in branched oligosaccharide
(Wed Mar 29 2017 - 05:32:14 PDT)
[AMBER] Oligosaccharide linkage breaking problem during Solvent minimization
(Wed Mar 29 2017 - 02:53:19 PDT)
[AMBER] Linkage problem in branched oligosaccharide
(Tue Mar 28 2017 - 05:36:34 PDT)
Maral Aminpour
[AMBER] Discrepancy between gaff.dat and leaprc.gaff hybridization
(Mon Mar 13 2017 - 13:17:52 PDT)
Marc van der Kamp
Re: [AMBER] restarting Amber calculations gives abnormal structures
(Fri Mar 31 2017 - 09:37:53 PDT)
Re: [AMBER] restarting Amber calculations gives abnormal structures
(Thu Mar 30 2017 - 23:58:25 PDT)
Marcos Serrou do Amaral
Re: [AMBER] Amber Mailing List problem
(Thu Mar 30 2017 - 07:02:09 PDT)
Markowska
Re: [AMBER] When does cpptraj use information from the original pdb file?
(Fri Mar 03 2017 - 09:57:56 PST)
Mary Varughese
Re: [AMBER] 2D rms plot doubt
(Sat Mar 18 2017 - 10:14:55 PDT)
[AMBER] 2D rms plot doubt
(Sat Mar 18 2017 - 02:56:00 PDT)
Maryam Hamzehee
[AMBER] problem with solvation
(Tue Mar 14 2017 - 00:21:18 PDT)
Michael Shokhen
Re: [AMBER] anionic Ser ?
(Thu Mar 09 2017 - 07:38:20 PST)
[AMBER] anionic Ser ?
(Thu Mar 09 2017 - 05:23:25 PST)
Miguel Garavís
Re: [AMBER] Problem with keyboard in xleap
(Wed Mar 22 2017 - 05:59:59 PDT)
Re: [AMBER] Problem with keyboard in xleap
(Wed Mar 22 2017 - 05:07:33 PDT)
[AMBER] Problem with keyboard in xleap
(Wed Mar 22 2017 - 03:59:30 PDT)
Miguel Rivera
[AMBER] pmemd.MPI error on lonestar5 super comp.
(Sun Mar 19 2017 - 15:48:00 PDT)
Ming Tang
Re: [AMBER] RDF plot
(Tue Mar 28 2017 - 03:41:17 PDT)
[AMBER] water bridge
(Tue Mar 28 2017 - 02:24:20 PDT)
Mingyuan_xu
[AMBER] Questions about MCPB.py
(Wed Mar 29 2017 - 18:57:03 PDT)
MOHD HOMAIDUR RAHMAN
Re: [AMBER] Water molecules show three bonds in VMD
(Thu Mar 30 2017 - 21:03:46 PDT)
Mrinal Arandhara
Re: [AMBER] dUMP parameters
(Sun Mar 05 2017 - 08:06:14 PST)
Re: [AMBER] dUMP parameters
(Sun Mar 05 2017 - 07:53:42 PST)
[AMBER] dUMP parameters
(Sun Mar 05 2017 - 07:20:35 PST)
nagakumarb.ccamp.res.in
[AMBER] residue contribution for covalent inhibitor
(Fri Mar 24 2017 - 06:54:34 PDT)
[AMBER] MM/GBSA residual decomposition issue
(Fri Mar 17 2017 - 08:13:20 PDT)
Neha Gandhi
[AMBER] cpptraj distance between centroid of a ring and an atom
(Thu Mar 23 2017 - 00:41:54 PDT)
Re: [AMBER] Accelerated MD
(Thu Mar 09 2017 - 04:46:09 PST)
[AMBER] Holes/bubbles in water during NVT (fix atoms)
(Tue Feb 28 2017 - 23:35:53 PST)
Nhai
Re: [AMBER] unable to solvate a polymer
(Wed Mar 22 2017 - 09:00:13 PDT)
Re: [AMBER] Error Importing pytraj to Python 2.7 Program
(Tue Mar 21 2017 - 15:31:31 PDT)
Re: [AMBER] Memory footprint goes on increasing: pytraj traj.iterchunk used, distances between bonds calculation
(Sun Mar 12 2017 - 13:41:00 PDT)
Re: [AMBER] AmberTools compilation
(Thu Mar 09 2017 - 05:51:03 PST)
Re: [AMBER] Distance between benzene ring of one molecule and centre of mass of other molecule
(Wed Mar 01 2017 - 17:38:36 PST)
Niel Henriksen
Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior
(Tue Mar 21 2017 - 13:50:00 PDT)
Nikolay N. Kuzmich
Re: [AMBER] Simulating a protein with modified amino acid residue, the saga continues. Atom ... does not have a type.
(Fri Mar 10 2017 - 08:35:09 PST)
[AMBER] Simulating a protein with modified amino acid residue, the saga continues. Atom ... does not have a type.
(Mon Mar 06 2017 - 09:16:33 PST)
Nirupma Singh
[AMBER] Issue regarding ligand parameterization
(Sun Mar 19 2017 - 22:55:18 PDT)
Oleksii Zdorevskyi
Re: [AMBER] converting trajectory file from NAMD to AMBER
(Thu Mar 16 2017 - 09:31:21 PDT)
Re: [AMBER] converting trajectory file from NAMD to AMBER
(Thu Mar 16 2017 - 08:40:12 PDT)
[AMBER] converting trajectory file from NAMD to AMBER
(Thu Mar 16 2017 - 07:43:12 PDT)
paul
Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16?
(Tue Mar 21 2017 - 04:35:39 PDT)
Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16?
(Mon Mar 20 2017 - 09:01:53 PDT)
[AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16?
(Mon Mar 20 2017 - 07:12:48 PDT)
[AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16?
(Mon Mar 20 2017 - 07:02:10 PDT)
Paul Westphaelinger
Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16
(Thu Mar 30 2017 - 12:46:48 PDT)
Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16?
(Tue Mar 28 2017 - 08:29:14 PDT)
Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16?
(Fri Mar 24 2017 - 01:53:43 PDT)
Paul Westphälinger
[AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16
(Thu Mar 30 2017 - 07:57:04 PDT)
Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16?
(Thu Mar 23 2017 - 03:38:38 PDT)
Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16?
(Wed Mar 22 2017 - 09:17:27 PDT)
Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16?
(Wed Mar 22 2017 - 00:42:22 PDT)
Re: [AMBER] Is it possible to create a bugreport.ambermd.org mailinglist?
(Wed Mar 22 2017 - 00:39:01 PDT)
[AMBER] Is it possible to create a bugreport.ambermd.org mailinglist?
(Tue Mar 21 2017 - 11:56:41 PDT)
Pengfei Li
Re: [AMBER] Error in Cobalt parameters in CO-METHYLCOBALAMIN with MCPB.py
(Tue Mar 14 2017 - 14:19:26 PDT)
Re: [AMBER] How to use MCPB.py to generate OH parameters
(Tue Mar 14 2017 - 14:09:38 PDT)
Re: [AMBER] prepare prepin file from MCPB results
(Mon Mar 06 2017 - 20:00:18 PST)
Ramin Salimi
Re: [AMBER] Issues Regaring the PDB files from Trajectory frames
(Fri Mar 31 2017 - 16:03:33 PDT)
Re: [AMBER] Issues Regaring the PDB files from Trajectory frames
(Fri Mar 31 2017 - 14:30:29 PDT)
[AMBER] Issues Regaring the PDB files from Trajectory frames
(Fri Mar 31 2017 - 14:23:52 PDT)
Re: [AMBER] Force/Energy vs extension curve from Steered MD
(Mon Mar 27 2017 - 11:13:07 PDT)
Re: [AMBER] Force/Energy vs extension curve from Steered MD
(Sun Mar 26 2017 - 21:48:49 PDT)
Re: [AMBER] Force/Energy vs extension curve from Steered MD
(Sun Mar 26 2017 - 14:21:49 PDT)
Re: [AMBER] Force/Energy vs extension curve from Steered MD
(Sat Mar 25 2017 - 12:05:03 PDT)
Re: [AMBER] Force/Energy vs extension curve from Steered MD
(Sat Mar 25 2017 - 11:15:19 PDT)
[AMBER] Force/Energy vs extension curve from Steered MD
(Sat Mar 25 2017 - 10:50:05 PDT)
[AMBER] Force/Energy vs extension curve from Steered MD
(Sat Mar 25 2017 - 10:36:15 PDT)
[AMBER] Force/energy vs extension curve in steered MD
(Sat Mar 25 2017 - 10:02:22 PDT)
Robin Jain
[AMBER] help in RDF
(Tue Mar 21 2017 - 08:19:44 PDT)
Ross Walker
Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior
(Thu Mar 23 2017 - 16:18:41 PDT)
Re: [AMBER] install AMBER16 GTX480
(Tue Mar 21 2017 - 17:09:38 PDT)
Re: [AMBER] pmemd.cuda and taskset on K80
(Wed Mar 01 2017 - 17:22:05 PST)
Sadegh Faramarzi Ganjabad
Re: [AMBER] restarting Amber calculations gives abnormal structures
(Thu Mar 30 2017 - 22:17:15 PDT)
Re: [AMBER] restarting Amber calculations gives abnormal structures
(Wed Mar 29 2017 - 12:26:56 PDT)
Re: [AMBER] restarting Amber calculations gives abnormal structures
(Tue Mar 28 2017 - 13:29:49 PDT)
[AMBER] restarting Amber calculations gives abnormal structures
(Sat Mar 25 2017 - 20:53:09 PDT)
[AMBER] Chamber error; No NONBONDED
(Wed Mar 22 2017 - 11:34:47 PDT)
[AMBER] Questions about Amber TI tutorial
(Tue Mar 21 2017 - 12:50:28 PDT)
Samuel Bowerman
Re: [AMBER] Error Importing pytraj to Python 2.7 Program
(Tue Mar 21 2017 - 15:05:00 PDT)
Re: [AMBER] Error Importing pytraj to Python 2.7 Program
(Tue Mar 21 2017 - 15:02:21 PDT)
[AMBER] Error Importing pytraj to Python 2.7 Program
(Tue Mar 21 2017 - 14:20:40 PDT)
Sangeetha B
Re: [AMBER] Linkage problem in branched oligosaccharide
(Wed Mar 29 2017 - 02:09:13 PDT)
Scott Brozell
Re: [AMBER] Installing Amber14 and AmberTools15 Error
(Thu Mar 30 2017 - 00:00:27 PDT)
Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior
(Thu Mar 23 2017 - 15:58:52 PDT)
[AMBER] multinode pmemd.cuda.MPI jac9999 behavior
(Tue Mar 21 2017 - 12:52:34 PDT)
SHAILESH KUMAR
Re: [AMBER] 2D rms plot doubt
(Mon Mar 20 2017 - 09:57:35 PDT)
Re: [AMBER] 2D rms plot doubt
(Sat Mar 18 2017 - 10:10:05 PDT)
Re: [AMBER] 2D rms plot doubt
(Sat Mar 18 2017 - 06:58:01 PDT)
Re: [AMBER] Memory footprint goes on increasing: pytraj traj.iterchunk used, distances between bonds calculation
(Sun Mar 12 2017 - 14:13:51 PDT)
[AMBER] Memory footprint goes on increasing: pytraj traj.iterchunk used, distances between bonds calculation
(Sun Mar 12 2017 - 13:17:30 PDT)
Re: [AMBER] Problem in configuring+compiling cpptraj development version with Sander compiled with AmberTools16
(Fri Mar 10 2017 - 07:51:54 PST)
Re: [AMBER] Problem in configuring+compiling cpptraj development version with Sander compiled with AmberTools16
(Fri Mar 10 2017 - 06:25:56 PST)
Re: [AMBER] Problem in configuring+compiling cpptraj development version with Sander compiled with AmberTools16
(Fri Mar 10 2017 - 05:35:04 PST)
[AMBER] Problem in configuring+compiling cpptraj development version with Sander compiled with AmberTools16
(Fri Mar 10 2017 - 02:50:34 PST)
Shanghaitech University WuMeng
[AMBER] Generate psf file for chamber
(Thu Mar 09 2017 - 02:56:23 PST)
Sidhu, Khushwant (Dr.)
[AMBER] distance calculations - Protein-RNA
(Thu Mar 16 2017 - 03:36:26 PDT)
Smriti Sharma
Re: [AMBER] reg "rel delta G binding computation using TIMD"
(Mon Mar 06 2017 - 19:37:43 PST)
[AMBER] reg "rel delta G binding computation using TIMD"
(Mon Mar 06 2017 - 02:12:32 PST)
Sofia Vasilakaki
[AMBER] Intel Xeon Phi 7120P
(Tue Mar 14 2017 - 07:26:43 PDT)
Sowmya Indrakumar
Re: [AMBER] FEW- issues generating parameter files for MD
(Wed Mar 29 2017 - 01:27:02 PDT)
Re: [AMBER] RDF plot
(Tue Mar 28 2017 - 11:17:06 PDT)
Re: [AMBER] RDF plot
(Tue Mar 28 2017 - 10:28:18 PDT)
Re: [AMBER] RDF plot
(Tue Mar 28 2017 - 10:04:57 PDT)
Re: [AMBER] RDF plot
(Tue Mar 28 2017 - 09:18:32 PDT)
Re: [AMBER] FEW- issues generating parameter files for MD
(Tue Mar 28 2017 - 08:59:19 PDT)
Re: [AMBER] FEW- issues generating parameter files for MD
(Tue Mar 28 2017 - 08:37:45 PDT)
Re: [AMBER] RDF plot
(Tue Mar 28 2017 - 06:03:19 PDT)
Re: [AMBER] RDF plot
(Tue Mar 28 2017 - 05:49:36 PDT)
Re: [AMBER] RDF plot
(Tue Mar 28 2017 - 03:51:28 PDT)
[AMBER] RDF plot
(Tue Mar 28 2017 - 03:35:39 PDT)
Re: [AMBER] FEW- issues generating parameter files for MD
(Mon Mar 27 2017 - 08:18:40 PDT)
[AMBER] FEW- issues generating parameter files for MD
(Mon Mar 27 2017 - 06:57:49 PDT)
[AMBER] Issue generating parameter files - FEW
(Tue Mar 21 2017 - 08:06:10 PDT)
[AMBER] issues generating parameter files for the ligands- FEW
(Fri Mar 17 2017 - 08:13:03 PDT)
Re: [AMBER] Issues running TI simulations
(Thu Mar 16 2017 - 05:21:07 PDT)
Re: [AMBER] Issues running TI simulations
(Thu Mar 16 2017 - 02:30:37 PDT)
[AMBER] Issues running TI simulations
(Thu Mar 16 2017 - 02:10:04 PDT)
Re: [AMBER] How to get parmed.py script?
(Wed Mar 15 2017 - 03:30:37 PDT)
[AMBER] How to get parmed.py script?
(Wed Mar 15 2017 - 02:31:05 PDT)
Re: [AMBER] how to use TImerge to do TI simulations
(Tue Mar 07 2017 - 07:44:46 PST)
Re: [AMBER] how to use TImerge to do TI simulations
(Tue Mar 07 2017 - 07:01:07 PST)
[AMBER] how to use TImerge to do TI simulations
(Tue Mar 07 2017 - 06:55:53 PST)
Stellamaris Sotomayor Burneo
[AMBER] OPEN SHELL MOLECULES
(Wed Mar 08 2017 - 14:19:29 PST)
Szymon Żaczek
[AMBER] Thermodynamic integration simulations issues
(Sun Mar 26 2017 - 13:02:04 PDT)
Thakur, Abhishek
[AMBER] renumber residues
(Fri Mar 24 2017 - 07:15:15 PDT)
[AMBER] hydophobic
(Thu Mar 09 2017 - 12:28:58 PST)
Re: [AMBER] Distance constraint
(Thu Mar 09 2017 - 07:53:35 PST)
Re: [AMBER] Simulating a protein with modified amino acid residue, the saga continues. Atom ... does not have a type.
(Mon Mar 06 2017 - 11:32:51 PST)
The Cromicus Productions
[AMBER] Count number of water molecules in minor groove of DNA
(Wed Mar 22 2017 - 12:33:02 PDT)
Thomas Evangelidis
Re: [AMBER] coordinates in restraint mast
(Fri Mar 31 2017 - 08:44:06 PDT)
Re: [AMBER] coordinates in restraint mast
(Fri Mar 31 2017 - 07:54:22 PDT)
[AMBER] coordinates in restraint mast
(Fri Mar 31 2017 - 06:13:37 PDT)
[AMBER] maximum distance for protein-ligand interactions in MM/GBSA
(Sat Mar 11 2017 - 07:34:05 PST)
Thomas Fox
Re: [AMBER] cpptraj: dihcovar and projection need trajin to work properly?
(Wed Mar 01 2017 - 09:54:04 PST)
Tom Dreyfus
Re: [AMBER] AmberTools compilation
(Thu Mar 09 2017 - 07:54:24 PST)
Re: [AMBER] AmberTools compilation
(Thu Mar 09 2017 - 07:36:09 PST)
Re: [AMBER] AmberTools compilation
(Thu Mar 09 2017 - 07:22:47 PST)
Re: [AMBER] AmberTools compilation
(Thu Mar 09 2017 - 06:41:44 PST)
Re: [AMBER] AmberTools compilation
(Thu Mar 09 2017 - 05:56:15 PST)
Re: [AMBER] AmberTools compilation
(Thu Mar 09 2017 - 05:45:18 PST)
[AMBER] AmberTools compilation
(Thu Mar 09 2017 - 05:04:44 PST)
Vaibhav Dixit
Re: [AMBER] RE : suitable basis sets for QM/MM
(Thu Mar 16 2017 - 22:01:28 PDT)
Vasantha Kumar
Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit
(Mon Mar 20 2017 - 08:49:48 PDT)
Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit
(Mon Mar 20 2017 - 08:38:01 PDT)
Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit
(Sat Mar 18 2017 - 19:19:19 PDT)
Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit
(Sat Mar 18 2017 - 19:12:19 PDT)
[AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit
(Fri Mar 17 2017 - 23:33:42 PDT)
Vijay Achari
[AMBER] Generating topology from Gaussian 09
(Thu Mar 16 2017 - 05:08:25 PDT)
Vishal Nemaysh
[AMBER] Split a Large trajectory into smaller trajectory
(Tue Mar 28 2017 - 21:30:33 PDT)
[AMBER] How to make rst file by using ptraj
(Sat Mar 04 2017 - 07:24:09 PST)
Vlad Cojocaru
Re: [AMBER] 发自刘兰茹的邮件
(Fri Mar 24 2017 - 06:50:38 PDT)
Re: [AMBER] 发自刘兰茹的邮件
(Fri Mar 24 2017 - 03:14:26 PDT)
Re: [AMBER] 发自刘兰茹的邮件
(Fri Mar 24 2017 - 01:53:00 PDT)
Yong Duan
Re: [AMBER] prepc vs prepi
(Tue Mar 14 2017 - 12:55:51 PDT)
[AMBER] prepc vs prepi
(Tue Mar 14 2017 - 12:36:07 PDT)
zengxitao
[AMBER] 来自zengxitao的邮件
(Wed Mar 22 2017 - 10:28:16 PDT)
刘兰茹
[AMBER] 发自刘兰茹的邮件
(Fri Mar 24 2017 - 01:42:12 PDT)
吴萌
[AMBER] Water molecules show three bonds in VMD
(Thu Mar 30 2017 - 04:04:57 PDT)
巩梦雪
Re: [AMBER] How to perform Newton-Raphson minimization to protein
(Fri Mar 24 2017 - 06:53:26 PDT)
[AMBER] How to perform Newton-Raphson minimization to protein
(Thu Mar 23 2017 - 05:22:59 PDT)
杨满意
[AMBER] Cpptraj problems
(Tue Mar 28 2017 - 20:43:52 PDT)
Re: [AMBER] How to generate inputfile
(Wed Mar 22 2017 - 05:48:51 PDT)
Re: [AMBER] How to generate inputfile (???)
(Fri Mar 17 2017 - 06:09:32 PDT)
Re: [AMBER] How to generate inputfile
(Fri Mar 17 2017 - 05:34:59 PDT)
Re: [AMBER] Problems in using Parmchk2
(Thu Mar 16 2017 - 07:13:06 PDT)
Re: [AMBER] Problems in using Parmchk2
(Wed Mar 15 2017 - 19:09:35 PDT)
Re: [AMBER] How to generate inputfile
(Wed Mar 15 2017 - 18:49:43 PDT)
[AMBER] Problems in using Parmchk2
(Wed Mar 15 2017 - 07:08:58 PDT)
[AMBER] How to generate inputfile
(Tue Mar 14 2017 - 20:37:08 PDT)
Re: [AMBER] Amber 16 MD simulation Problems
(Mon Mar 06 2017 - 03:38:14 PST)
Re: [AMBER] Amber 16 MD simulation Problems
(Mon Mar 06 2017 - 02:53:46 PST)
[AMBER] Amber 16 MD simulation Problems
(Sat Mar 04 2017 - 20:11:03 PST)
鲁俊波
[AMBER] Error when running QM/MM MD for actinide and lanthanide system by amber
(Mon Mar 13 2017 - 19:22:19 PDT)
Last message date
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Fri Mar 31 2017 - 16:30:03 PDT
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: Wed Dec 25 2024 - 05:55:29 PST
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