Amber Archive Dec 2017: by thread

[AMBER] Error: No module named parmed.scripts Setyanto Md (Thu Nov 30 2017 - 15:12:49 PST)
- Re: [AMBER] Error: No module named parmed.scripts Jason Swails (Sun Dec 03 2017 - 20:43:17 PST)
  - Re: [AMBER] Error: No module named parmed.scripts Setyanto Md (Mon Dec 04 2017 - 06:50:00 PST)
[AMBER] Problems with the "conbine" conmmand in LEaP 杨满意 (Thu Nov 30 2017 - 16:56:33 PST)
- Re: [AMBER] Problems with the "conbine" conmmand in LEaP Daniel Roe (Fri Dec 01 2017 - 05:30:14 PST)
  - Re: [AMBER] Problems with the "conbine" conmmand in LEaP 杨满意 (Fri Dec 01 2017 - 17:23:16 PST)
Re: [AMBER] imin=5 not working in AMBER16? Paul Mortenson (Thu Nov 30 2017 - 23:52:26 PST)
- Re: [AMBER] imin=5 not working in AMBER16? Daniel Roe (Fri Dec 01 2017 - 05:39:05 PST)
  - Re: [AMBER] imin=5 not working in AMBER16? Paul Mortenson (Fri Dec 01 2017 - 07:08:44 PST)
- Re: [AMBER] imin=5 not working in AMBER16? David A Case (Fri Dec 01 2017 - 09:40:52 PST)
  - Re: [AMBER] imin=5 not working in AMBER16? Paul Mortenson (Mon Dec 04 2017 - 06:04:04 PST)
Re: [AMBER] PF6- octahedral geometry change during equilibration!! Gustavo Seabra (Fri Dec 01 2017 - 03:23:40 PST)
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! Junmei Wang (Fri Dec 01 2017 - 09:29:41 PST)
  - Re: [AMBER] PF6- octahedral geometry change during equilibration!! Sanaa ALAbbad (Fri Dec 01 2017 - 09:41:17 PST)
    - Re: [AMBER] PF6- octahedral geometry change during equilibration!! Sanaa ALAbbad (Fri Dec 01 2017 - 11:13:57 PST)
    - Re: [AMBER] PF6- octahedral geometry change during equilibration!! Junmei Wang (Fri Dec 01 2017 - 11:30:46 PST)
    - Re: [AMBER] PF6- octahedral geometry change during equilibration!! mirzo (Fri Dec 01 2017 - 11:43:57 PST)
    - Re: [AMBER] PF6- octahedral geometry change during equilibration!! Sanaa ALAbbad (Fri Dec 01 2017 - 15:54:41 PST)
[AMBER] implicit models for other solvents and non-standard solvents Vaibhav Dixit (Fri Dec 01 2017 - 04:35:11 PST)
Re: [AMBER] antechamber: prepgen mainchain file character limit Junmei Wang (Fri Dec 01 2017 - 11:35:35 PST)
[AMBER] Residue Protonation State Rana Rehan Khalid (Sat Dec 02 2017 - 01:07:50 PST)
- Re: [AMBER] Residue Protonation State Schmid, Ralf (Dr.) (Sat Dec 02 2017 - 09:08:40 PST)
[AMBER] lipid 14 compatibility with FF14SB Chitrak Gupta (Sat Dec 02 2017 - 11:17:33 PST)
- Re: [AMBER] lipid 14 compatibility with FF14SB David A Case (Sun Dec 03 2017 - 05:39:45 PST)
[AMBER] Problem with running Example2 from MCPB.py reference SI file MinYuan (Sat Dec 02 2017 - 19:25:29 PST)
- Re: [AMBER] Problem with running Example2 from MCPB.py reference SI file Pengfei Li (Mon Dec 04 2017 - 14:12:11 PST)
  - Re: [AMBER] Problem with running Example2 from MCPB.py reference SI file MinYuan (Tue Dec 05 2017 - 03:33:18 PST)
[AMBER] MCPB.py to generate force field parameter for metal ion As3+ MinYuan (Sat Dec 02 2017 - 19:49:17 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Lorenzo Gontrani (Sun Dec 03 2017 - 02:19:42 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ minyuan.mail.ustc.edu.cn (Sun Dec 03 2017 - 02:33:18 PST)
  - Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Lorenzo Gontrani (Sun Dec 03 2017 - 02:49:49 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Lorenzo Gontrani (Sun Dec 03 2017 - 02:51:17 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ minyuan.mail.ustc.edu.cn (Sun Dec 03 2017 - 02:56:59 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Lorenzo Gontrani (Sun Dec 03 2017 - 03:10:43 PST)
  - Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ MinYuan (Sun Dec 03 2017 - 03:57:24 PST)
    - Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Pengfei Li (Mon Dec 04 2017 - 14:07:12 PST)
    - Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ MinYuan (Mon Dec 04 2017 - 18:09:03 PST)
    - Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ MinYuan (Mon Dec 04 2017 - 18:12:48 PST)
    - Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Lorenzo Gontrani (Mon Dec 04 2017 - 22:17:54 PST)
    - Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ MinYuan (Tue Dec 05 2017 - 03:31:48 PST)
[AMBER] Normalization of radial distribution function Szymon Żaczek (Sun Dec 03 2017 - 10:38:08 PST)
- Re: [AMBER] Normalization of radial distribution function George M. Giambasu (Mon Dec 04 2017 - 07:28:33 PST)
  - Re: [AMBER] Normalization of radial distribution function Szymon Żaczek (Tue Dec 05 2017 - 00:09:38 PST)
    - Re: [AMBER] Normalization of radial distribution function Batuhan Kav (Tue Dec 05 2017 - 01:40:54 PST)
    - Re: [AMBER] Normalization of radial distribution function Szymon Żaczek (Tue Dec 05 2017 - 03:31:08 PST)
[AMBER] helix broken during minimization step Rana Rehan Khalid (Mon Dec 04 2017 - 06:52:34 PST)
[AMBER] GPU workstation with 8 x nVidia GTX 1080 Ti Hadházi Ádám (Mon Dec 04 2017 - 10:41:10 PST)
- Re: [AMBER] GPU workstation with 8 x nVidia GTX 1080 Ti Ross Walker (Mon Dec 04 2017 - 10:48:15 PST)
- Re: [AMBER] GPU workstation with 8 x nVidia GTX 1080 Ti Carlos Simmerling (Mon Dec 04 2017 - 11:32:22 PST)
  - Re: [AMBER] GPU workstation with 8 x nVidia GTX 1080 Ti Ross Walker (Mon Dec 04 2017 - 11:38:14 PST)
Re: [AMBER] MCPB.py how to insert the heteroatom heme in the one domain of macromolecule Pengfei Li (Mon Dec 04 2017 - 14:22:19 PST)
[AMBER] To calculate TI using soft-core potential or not Yang Jinpeng (Tue Dec 05 2017 - 00:35:09 PST)
- Re: [AMBER] To calculate TI using soft-core potential or not Daniel Mermelstein (Tue Dec 05 2017 - 13:54:40 PST)
[AMBER] how to generate paramaters for GlcNH3 Tarsis (Tue Dec 05 2017 - 14:19:25 PST)
- Re: [AMBER] how to generate paramaters for GlcNH3 Bill Ross (Tue Dec 05 2017 - 14:29:28 PST)
- Re: [AMBER] how to generate paramaters for GlcNH3 Tarsis (Thu Dec 07 2017 - 11:37:09 PST)
- Re: [AMBER] how to generate paramaters for GlcNH3 Tarsis Ferreira (Fri Dec 08 2017 - 09:34:17 PST)
  - Re: [AMBER] how to generate paramaters for GlcNH3 Lachele Foley (Fri Dec 08 2017 - 15:01:39 PST)
[AMBER] generation of topology and coordinate for glycan Rajarshi Roy (Tue Dec 05 2017 - 20:56:41 PST)
- Re: [AMBER] generation of topology and coordinate for glycan Bill Ross (Tue Dec 05 2017 - 21:15:08 PST)
  - Re: [AMBER] generation of topology and coordinate for glycan Rajarshi Roy (Tue Dec 05 2017 - 22:14:02 PST)
    - Re: [AMBER] generation of topology and coordinate for glycan Bill Ross (Tue Dec 05 2017 - 22:32:03 PST)
    - Re: [AMBER] generation of topology and coordinate for glycan Lachele Foley (Thu Dec 07 2017 - 19:09:31 PST)
[AMBER] Problem in visualizing Amber16 trajecories in VMD Biplab Ghosh (Tue Dec 05 2017 - 22:57:23 PST)
- Re: [AMBER] Problem in visualizing Amber16 trajecories in VMD Bill Ross (Tue Dec 05 2017 - 23:11:14 PST)
  - Re: [AMBER] Problem in visualizing Amber16 trajecories in VMD Abdul-Rashid III Sampaco (Tue Dec 05 2017 - 23:55:18 PST)
- Re: [AMBER] Problem in visualizing Amber16 trajecories in VMD David A Case (Wed Dec 06 2017 - 05:08:36 PST)
[AMBER] Amber Protonate for H++ Andreas Tosstorff (Wed Dec 06 2017 - 09:58:19 PST)
- Re: [AMBER] Amber Protonate for H++ David A Case (Wed Dec 06 2017 - 11:14:48 PST)
  - Re: [AMBER] Amber Protonate for H++ Andreas Tosstorff (Thu Dec 07 2017 - 01:45:03 PST)
    - Re: [AMBER] Amber Protonate for H++ David A Case (Fri Dec 08 2017 - 06:14:58 PST)
- Re: [AMBER] Amber Protonate for H++ Setyanto Md (Wed Dec 06 2017 - 19:17:44 PST)
  - Re: [AMBER] Amber Protonate for H++ Andreas Tosstorff (Thu Dec 07 2017 - 00:28:16 PST)
    - Re: [AMBER] Amber Protonate for H++ Setyanto Md (Thu Dec 07 2017 - 05:30:43 PST)
[AMBER] The paramters of frcmod.chcl3 Yang Jinpeng (Wed Dec 06 2017 - 19:25:50 PST)
[AMBER] force addions to avoid replacing specific solvent molecules by ions Vlad Cojocaru (Thu Dec 07 2017 - 02:14:41 PST)
- Re: [AMBER] force addions to avoid replacing specific solvent molecules by ions Bill Ross (Thu Dec 07 2017 - 02:24:31 PST)
  - Re: [AMBER] force addions to avoid replacing specific solvent molecules by ions Vlad Cojocaru (Thu Dec 07 2017 - 02:35:58 PST)
    - Re: [AMBER] force addions to avoid replacing specific solvent molecules by ions Bill Ross (Thu Dec 07 2017 - 02:39:20 PST)
    - Re: [AMBER] force addions to avoid replacing specific solvent molecules by ions Vlad Cojocaru (Thu Dec 07 2017 - 02:52:10 PST)
[AMBER] Modified amino acid Rajarshi Roy (Thu Dec 07 2017 - 03:37:22 PST)
- Re: [AMBER] Modified amino acid junmwang.gmail.com (Thu Dec 07 2017 - 04:29:44 PST)
  - Re: [AMBER] Modified amino acid Rajarshi Roy (Thu Dec 07 2017 - 05:25:20 PST)
    - Re: [AMBER] Modified amino acid Junmei Wang (Thu Dec 07 2017 - 07:49:49 PST)
    - Re: [AMBER] Modified amino acid Rajarshi Roy (Fri Dec 08 2017 - 02:24:06 PST)
[AMBER] pdf of O-GlcNAc Ser and Thr Yin, Guowei (Thu Dec 07 2017 - 07:57:35 PST)
- [AMBER] pdf of O-GlcNAc Ser and Thr Yin, Guowei (Thu Dec 07 2017 - 09:42:50 PST)
[AMBER] End-of-File error occurring for Minimization run using Amoeba Force Field Chase Zagorec-Marks (Thu Dec 07 2017 - 09:48:28 PST)
- Re: [AMBER] End-of-File error occurring for Minimization run using Amoeba Force Field David A Case (Fri Dec 08 2017 - 06:24:29 PST)
[AMBER] pdf of O-GlcNAc Ser and Thr Li, Xinghui (Thu Dec 07 2017 - 11:15:07 PST)
- Re: [AMBER] pdf of O-GlcNAc Ser and Thr Lachele Foley (Thu Dec 07 2017 - 19:11:34 PST)
[AMBER] Bonds between residues are broken Shilpa Gupta (Thu Dec 07 2017 - 21:33:59 PST)
- Re: [AMBER] Bonds between residues are broken David A Case (Fri Dec 08 2017 - 06:27:28 PST)
  - Re: [AMBER] Bonds between residues are broken Shilpa Gupta (Fri Dec 08 2017 - 08:22:18 PST)
[AMBER] Does pmemd.cuda support QM/MM MinYuan (Fri Dec 08 2017 - 00:03:47 PST)
- Re: [AMBER] Does pmemd.cuda support QM/MM Elvis Martis (Fri Dec 08 2017 - 02:27:12 PST)
  - Re: [AMBER] Does pmemd.cuda support QM/MM MinYuan (Sat Dec 09 2017 - 04:15:03 PST)
    - Re: [AMBER] Does pmemd.cuda support QM/MM Rivera, Miguel (Tue Dec 12 2017 - 04:20:32 PST)
    - Re: [AMBER] Does pmemd.cuda support QM/MM David Cerutti (Tue Dec 12 2017 - 05:01:19 PST)
    - Re: [AMBER] Does pmemd.cuda support QM/MM Elvis Martis (Tue Dec 12 2017 - 05:03:18 PST)
Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Dow Hurst (Fri Dec 08 2017 - 11:34:47 PST)
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER David Cerutti (Fri Dec 08 2017 - 12:18:39 PST)
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Ross Walker (Sat Dec 09 2017 - 09:53:31 PST)
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Scott Le Grand (Sat Dec 09 2017 - 11:35:18 PST)
[AMBER] Problem of loading complex Mustafa Alhaji Isa (Fri Dec 08 2017 - 12:48:55 PST)
- Re: [AMBER] Problem of loading complex Carlos Simmerling (Fri Dec 08 2017 - 12:51:33 PST)
  - Re: [AMBER] Problem of loading complex Mustafa Alhaji Isa (Fri Dec 08 2017 - 13:08:31 PST)
    - Re: [AMBER] Problem of loading complex Carlos Simmerling (Fri Dec 08 2017 - 15:19:01 PST)
    - Re: [AMBER] Problem of loading complex David A Case (Fri Dec 08 2017 - 17:51:32 PST)
[AMBER] Solvating a molecule in amber Shilpa Gupta (Sun Dec 10 2017 - 20:37:41 PST)
- Re: [AMBER] Solvating a molecule in amber Bill Ross (Sun Dec 10 2017 - 22:05:02 PST)
  - Re: [AMBER] Solvating a molecule in amber Shilpa Gupta (Sun Dec 10 2017 - 22:09:28 PST)
    - Re: [AMBER] Solvating a molecule in amber Bill Ross (Sun Dec 10 2017 - 22:42:52 PST)
    - Re: [AMBER] Solvating a molecule in amber Shilpa Gupta (Mon Dec 11 2017 - 04:20:48 PST)
    - Re: [AMBER] Solvating a molecule in amber Bill Ross (Mon Dec 11 2017 - 05:05:31 PST)
    - Re: [AMBER] Solvating a molecule in amber Shilpa Gupta (Mon Dec 11 2017 - 05:17:58 PST)
[AMBER] Queries about aMD simulation of metal-bound membrane protein and anu chandra (Mon Dec 11 2017 - 01:59:43 PST)
[AMBER] MCPB HEME Rana Rehan Khalid (Mon Dec 11 2017 - 03:00:11 PST)
- Re: [AMBER] MCPB HEME Bill Ross (Mon Dec 11 2017 - 03:02:14 PST)
- Re: [AMBER] MCPB HEME Marcos Serrou do Amaral (Mon Dec 11 2017 - 05:53:14 PST)
  - Re: [AMBER] MCPB HEME Rana Rehan Khalid (Mon Dec 11 2017 - 06:33:52 PST)
[AMBER] cpptraj segmentation fault Andreas Tosstorff (Mon Dec 11 2017 - 07:12:31 PST)
- Re: [AMBER] cpptraj segmentation fault Daniel Roe (Mon Dec 11 2017 - 07:41:10 PST)
  - Re: [AMBER] cpptraj segmentation fault Andreas Tosstorff (Mon Dec 11 2017 - 07:47:12 PST)
    - Re: [AMBER] cpptraj segmentation fault Daniel Roe (Mon Dec 11 2017 - 07:53:48 PST)
    - Re: [AMBER] cpptraj segmentation fault Andreas Tosstorff (Mon Dec 11 2017 - 08:07:21 PST)
    - Re: [AMBER] cpptraj segmentation fault Daniel Roe (Mon Dec 11 2017 - 08:38:35 PST)
    - Re: [AMBER] cpptraj segmentation fault Daniel Roe (Mon Dec 11 2017 - 08:39:22 PST)
[AMBER] MCPB.py deal with two metal-like sites simultaneously MinYuan (Tue Dec 12 2017 - 02:14:52 PST)
- Re: [AMBER] MCPB.py deal with two metal-like sites simultaneously Pengfei Li (Wed Dec 13 2017 - 08:54:11 PST)
[AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Myron (Tue Dec 12 2017 - 04:26:16 PST)
- Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Carlos Simmerling (Tue Dec 12 2017 - 05:23:38 PST)
  - Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Myron (Tue Dec 12 2017 - 08:07:10 PST)
    - Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Carlos Simmerling (Tue Dec 12 2017 - 09:39:28 PST)
- Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Daniel Roe (Tue Dec 12 2017 - 05:52:05 PST)
  - Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Myron (Tue Dec 12 2017 - 08:15:48 PST)
[AMBER] error when running tleap from script, works fine from shell Andreas Tosstorff (Tue Dec 12 2017 - 05:52:58 PST)
- Re: [AMBER] error when running tleap from script, works fine from shell David A Case (Wed Dec 13 2017 - 06:14:30 PST)
[AMBER] MMPBSA.py and S-S bonds between different chains Sergey Samsonov (Tue Dec 12 2017 - 07:58:59 PST)
[AMBER] Error with installation, amber 17 on centos server Praneeth Bommisetti (Tue Dec 12 2017 - 09:16:03 PST)
- Re: [AMBER] Error with installation, amber 17 on centos server Hai Nguyen (Tue Dec 12 2017 - 09:22:14 PST)
- Re: [AMBER] Error with installation, amber 17 on centos server Tru Huynh (Tue Dec 12 2017 - 10:23:34 PST)
[AMBER] Fwd: Re: Error with installation, amber 17 on centos server Praneeth Bommisetti (Tue Dec 12 2017 - 10:05:54 PST)
[AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib MinYuan (Tue Dec 12 2017 - 19:11:20 PST)
- Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib Pengfei Li (Wed Dec 13 2017 - 08:54:52 PST)
  - Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib MinYuan (Fri Dec 15 2017 - 06:04:19 PST)
    - Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib Bill Ross (Fri Dec 15 2017 - 06:12:23 PST)
    - Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib Pengfei Li (Fri Dec 15 2017 - 07:58:53 PST)
- Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib minyuan.mail.ustc.edu.cn (Sun Dec 17 2017 - 22:49:02 PST)
  - Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib Pengfei Li (Wed Dec 20 2017 - 14:57:29 PST)
[AMBER] Parmed topology file have ifbox=0 Shilpa Gupta (Wed Dec 13 2017 - 00:36:57 PST)
[AMBER] MM-GBSA, acquire the value of each frame Giovanni Grazioso (Wed Dec 13 2017 - 07:56:30 PST)
- Re: [AMBER] MM-GBSA, acquire the value of each frame Casalini Tommaso (Wed Dec 13 2017 - 08:00:26 PST)
- Re: [AMBER] MM-GBSA, acquire the value of each frame Dolivier (Wed Dec 13 2017 - 08:00:47 PST)
[AMBER] T.I. Sidechain setup (softcore potential) based off of A9 tutorial Andrew Schaub (Wed Dec 13 2017 - 11:17:58 PST)
- Re: [AMBER] T.I. Sidechain setup (softcore potential) based off of A9 tutorial Daniel Mermelstein (Sun Dec 17 2017 - 14:49:24 PST)
[AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Wed Dec 13 2017 - 13:58:26 PST)
- Re: [AMBER] PCA.CPPTRAJ Daniel Roe (Thu Dec 14 2017 - 10:21:41 PST)
  - Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Thu Dec 14 2017 - 13:03:41 PST)
    - Re: [AMBER] PCA.CPPTRAJ Daniel Roe (Fri Dec 15 2017 - 06:39:03 PST)
  - Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Sat Dec 16 2017 - 00:05:12 PST)
    - Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Sat Dec 16 2017 - 05:38:13 PST)
    - Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Sat Dec 16 2017 - 07:25:38 PST)
    - Re: [AMBER] PCA.CPPTRAJ Daniel Roe (Mon Dec 18 2017 - 10:58:06 PST)
    - Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Mon Dec 18 2017 - 13:16:27 PST)
    - Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Mon Dec 18 2017 - 13:43:33 PST)
    - Re: [AMBER] PCA.CPPTRAJ Daniel Roe (Tue Dec 19 2017 - 06:23:37 PST)
    - Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Tue Dec 19 2017 - 06:24:51 PST)
    - Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Thu Dec 21 2017 - 04:36:13 PST)
Re: [AMBER] autoimage for a protein filament Baker, Joseph (Wed Dec 13 2017 - 14:32:59 PST)
- Re: [AMBER] autoimage for a protein filament Daniel Roe (Thu Dec 14 2017 - 07:30:50 PST)
  - Re: [AMBER] autoimage for a protein filament Baker, Joseph (Sat Dec 16 2017 - 15:56:43 PST)
[AMBER] query regarding restraint_wt Leena Aggarwal (Thu Dec 14 2017 - 01:57:34 PST)
- Re: [AMBER] query regarding restraint_wt Bill Ross (Thu Dec 14 2017 - 02:15:21 PST)
  - Re: [AMBER] query regarding restraint_wt Leena Aggarwal (Thu Dec 14 2017 - 02:18:42 PST)
    - Re: [AMBER] query regarding restraint_wt Bill Ross (Thu Dec 14 2017 - 02:24:56 PST)
    - Re: [AMBER] query regarding restraint_wt Carlos Simmerling (Thu Dec 14 2017 - 03:51:48 PST)
[AMBER] TI softcore single topology (HIE to HIP) - How do I generate a new lib file for an existing residue? Andrew Schaub (Thu Dec 14 2017 - 09:58:50 PST)
- Re: [AMBER] TI softcore single topology (HIE to HIP) - How do I generate a new lib file for an existing residue? Andrew Schaub (Thu Dec 14 2017 - 10:03:56 PST)
  - Re: [AMBER] TI softcore single topology (HIE to HIP) - How do I generate a new lib file for an existing residue? Andrew Schaub (Thu Dec 14 2017 - 10:28:42 PST)
[AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords Investigador Química (Thu Dec 14 2017 - 16:42:23 PST)
- Re: [AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords David A Case (Fri Dec 15 2017 - 05:43:20 PST)
  - Re: [AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords Elvis Martis (Fri Dec 15 2017 - 06:07:14 PST)
  - Re: [AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords Investigador Química (Tue Dec 19 2017 - 03:27:19 PST)
[AMBER] HREMD run Dr. MANAS MONDAL (Thu Dec 14 2017 - 17:47:56 PST)
- Re: [AMBER] HREMD run Daniel Roe (Fri Dec 15 2017 - 06:38:10 PST)
  - Re: [AMBER] HREMD run Dr. MANAS MONDAL (Mon Dec 18 2017 - 03:28:23 PST)
    - Re: [AMBER] HREMD run Daniel Roe (Mon Dec 18 2017 - 10:50:19 PST)
    - Re: [AMBER] HREMD run Dr. MANAS MONDAL (Mon Dec 18 2017 - 18:32:45 PST)
    - Re: [AMBER] HREMD run Hai Nguyen (Mon Dec 18 2017 - 18:40:45 PST)
[AMBER] Leap not running Naina Singh (Sat Dec 16 2017 - 04:10:18 PST)
- Re: [AMBER] Leap not running Bill Ross (Sat Dec 16 2017 - 04:13:02 PST)
- Re: [AMBER] Leap not running David A Case (Sat Dec 16 2017 - 05:20:35 PST)
[AMBER] CPPTRAJ hbond Analysis Rana Rehan Khalid (Sun Dec 17 2017 - 13:17:13 PST)
- Re: [AMBER] CPPTRAJ hbond Analysis Hai Nguyen (Mon Dec 18 2017 - 02:47:52 PST)
  - Re: [AMBER] CPPTRAJ hbond Analysis Rana Rehan Khalid (Mon Dec 18 2017 - 03:04:23 PST)
    - Re: [AMBER] CPPTRAJ hbond Analysis Daniel Roe (Mon Dec 18 2017 - 10:52:03 PST)
    - Re: [AMBER] CPPTRAJ hbond Analysis Rana Rehan Khalid (Mon Dec 18 2017 - 14:36:49 PST)
    - Re: [AMBER] CPPTRAJ hbond Analysis Daniel Roe (Tue Dec 19 2017 - 06:23:10 PST)
    - Re: [AMBER] CPPTRAJ hbond Analysis Rana Rehan Khalid (Wed Dec 20 2017 - 08:05:26 PST)
[AMBER] cpptraj multiple trajectories Andreas Tosstorff (Mon Dec 18 2017 - 02:14:31 PST)
- Re: [AMBER] cpptraj multiple trajectories Daniel Roe (Mon Dec 18 2017 - 10:48:15 PST)
[AMBER] Several questions about Amber adaptive QM/MM MD. Mingyuan_xu (Mon Dec 18 2017 - 08:39:00 PST)
- Re: [AMBER] Several questions about Amber adaptive QM/MM MD. Goetz, Andreas (Fri Dec 22 2017 - 17:45:39 PST)
[AMBER] Water-slab at constant pressure jesus berlanga (Mon Dec 18 2017 - 18:38:52 PST)
- Re: [AMBER] Water-slab at constant pressure David A Case (Tue Dec 19 2017 - 05:21:58 PST)
[AMBER] box coordinates of the trajectory Leena Aggarwal (Mon Dec 18 2017 - 20:44:32 PST)
- Re: [AMBER] box coordinates of the trajectory Bill Ross (Mon Dec 18 2017 - 20:47:51 PST)
- [AMBER] [MGMS-DS]: Molecular Modelling Workshop March 12-14, 2018 in Erlangen, Germany Dr. Anselm Horn (Tue Dec 19 2017 - 01:36:28 PST)
- Re: [AMBER] box coordinates of the trajectory Daniel Roe (Tue Dec 19 2017 - 06:19:43 PST)
[AMBER] more than 100% hydrogen bond population Thakur, Abhishek (Wed Dec 20 2017 - 12:38:59 PST)
[AMBER] error in distance restraints Michael Shokhen (Wed Dec 20 2017 - 13:40:03 PST)
- Re: [AMBER] error in distance restraints David A Case (Wed Dec 20 2017 - 18:53:56 PST)
[AMBER] Function name not recognized in RdPar Rinsha Chk (Thu Dec 21 2017 - 00:24:53 PST)
- Re: [AMBER] Function name not recognized in RdPar David A Case (Thu Dec 21 2017 - 05:13:14 PST)
  - Re: [AMBER] Function name not recognized in RdPar Rinsha Chk (Thu Dec 21 2017 - 05:20:48 PST)
    - Re: [AMBER] Function name not recognized in RdPar Rinsha Chk (Thu Dec 21 2017 - 05:21:45 PST)
[AMBER] parmed error Thakur, Abhishek (Thu Dec 21 2017 - 10:44:56 PST)
- Re: [AMBER] parmed error p.kartheek (Thu Dec 21 2017 - 11:26:16 PST)
- Re: [AMBER] parmed error Hai Nguyen (Thu Dec 21 2017 - 18:53:52 PST)
[AMBER] Binding energy of ligand with homology model Morrow,John Kenneth (Thu Dec 21 2017 - 11:45:31 PST)
[AMBER] Atom restraints in AMBER Nikolay N. Kuzmich (Fri Dec 22 2017 - 00:29:09 PST)
[AMBER] Meltcurve cpptraj Andreas Tosstorff (Fri Dec 22 2017 - 02:17:26 PST)
- Re: [AMBER] Meltcurve cpptraj Daniel Roe (Fri Dec 22 2017 - 05:34:42 PST)
[AMBER] hbond occupancy plot cpptraj Rana Rehan Khalid (Sat Dec 23 2017 - 17:38:35 PST)
- Re: [AMBER] hbond occupancy plot cpptraj Rana Rehan Khalid (Sun Dec 24 2017 - 04:45:38 PST)
[AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Tue Dec 26 2017 - 00:09:35 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? David Cerutti (Tue Dec 26 2017 - 06:12:01 PST)
  - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Tue Dec 26 2017 - 16:12:02 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Bill Ross (Tue Dec 26 2017 - 16:14:03 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Tue Dec 26 2017 - 16:27:32 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley (Tue Dec 26 2017 - 19:51:32 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Tue Dec 26 2017 - 20:10:40 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley (Tue Dec 26 2017 - 20:22:42 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Tue Dec 26 2017 - 20:36:44 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley (Tue Dec 26 2017 - 20:42:38 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Tue Dec 26 2017 - 20:56:13 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Bill Ross (Tue Dec 26 2017 - 21:06:38 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Tue Dec 26 2017 - 21:09:11 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley (Wed Dec 27 2017 - 00:36:04 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Bill Ross (Wed Dec 27 2017 - 00:44:40 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley (Wed Dec 27 2017 - 00:55:41 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Wed Dec 27 2017 - 04:23:05 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley (Wed Dec 27 2017 - 22:46:35 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Thu Dec 28 2017 - 00:49:43 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley (Thu Dec 28 2017 - 22:30:44 PST)
[AMBER] Fwd: A small but fatal Typo in "LEaP Tutorial" Gao Zhenting (Tue Dec 26 2017 - 01:01:24 PST)
- Re: [AMBER] A small but fatal Typo in "LEaP Tutorial" Pengfei Li (Tue Dec 26 2017 - 09:49:18 PST)
  - Re: [AMBER] A small but fatal Typo in "LEaP Tutorial" Gao Zhenting (Tue Dec 26 2017 - 18:16:48 PST)
[AMBER] Unable to compile mixed C/Fortran code. suma jayakrishnan (Tue Dec 26 2017 - 03:53:18 PST)
- Re: [AMBER] Unable to compile mixed C/Fortran code. Bill Ross (Tue Dec 26 2017 - 04:18:48 PST)
- Re: [AMBER] Unable to compile mixed C/Fortran code. David A Case (Tue Dec 26 2017 - 06:04:03 PST)
[AMBER] Troubling changes to NVIDIA Driver EULA Ross Walker (Tue Dec 26 2017 - 08:07:25 PST)
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA Charles-Alexandre Mattelaer (Tue Dec 26 2017 - 08:29:27 PST)
  - Re: [AMBER] Troubling changes to NVIDIA Driver EULA David Cerutti (Tue Dec 26 2017 - 09:54:02 PST)
  - Re: [AMBER] Troubling changes to NVIDIA Driver EULA Ross Walker (Tue Dec 26 2017 - 11:57:10 PST)
    - Re: [AMBER] Troubling changes to NVIDIA Driver EULA David Cerutti (Tue Dec 26 2017 - 12:11:26 PST)
    - Re: [AMBER] Troubling changes to NVIDIA Driver EULA Ross Walker (Tue Dec 26 2017 - 15:43:22 PST)
    - Re: [AMBER] Troubling changes to NVIDIA Driver EULA Bill Ross (Tue Dec 26 2017 - 16:01:20 PST)
    - Re: [AMBER] Troubling changes to NVIDIA Driver EULA Robert Molt (Tue Dec 26 2017 - 17:24:57 PST)
    - Re: [AMBER] Troubling changes to NVIDIA Driver EULA Bill Ross (Tue Dec 26 2017 - 16:09:58 PST)
[AMBER] Which potential is used in TIP3P (How to calculate EPot by hand) Johannes Kalliauer (Wed Dec 27 2017 - 05:00:32 PST)
- Re: [AMBER] Which potential is used in TIP3P (How to calculate EPot by hand) David Cerutti (Wed Dec 27 2017 - 05:34:42 PST)
- Re: [AMBER] Which potential is used in TIP3P (How to calculate EPot by hand) David A Case (Wed Dec 27 2017 - 06:00:58 PST)
[AMBER] NTWR,NTWX, NTPR increases for rest of simulation. Rana Rehan Khalid (Wed Dec 27 2017 - 12:47:14 PST)
- Re: [AMBER] NTWR,NTWX, NTPR increases for rest of simulation. David A Case (Wed Dec 27 2017 - 14:16:55 PST)
  - Re: [AMBER] NTWR,NTWX, NTPR increases for rest of simulation. Rana Rehan Khalid (Wed Dec 27 2017 - 14:19:44 PST)
[AMBER] Phosphohistidine residues Jan Ludwiczak (Thu Dec 28 2017 - 08:34:50 PST)
[AMBER] CPPTRAJ HBOND Rana Rehan Khalid (Fri Dec 29 2017 - 05:40:31 PST)
- Re: [AMBER] CPPTRAJ HBOND Daniel Roe (Fri Dec 29 2017 - 05:51:28 PST)
  - Re: [AMBER] CPPTRAJ HBOND Charles-Alexandre Mattelaer (Fri Dec 29 2017 - 05:58:47 PST)
    - Re: [AMBER] CPPTRAJ HBOND Rana Rehan Khalid (Fri Dec 29 2017 - 08:26:26 PST)
[AMBER] DSSP CPPtraj Rana Rehan Khalid (Sun Dec 31 2017 - 06:27:35 PST)
- Re: [AMBER] DSSP CPPtraj Rana Rehan Khalid (Sun Dec 31 2017 - 07:05:20 PST)

Amber Archive Dec 2017 by thread