Amber Archive Sep 2017: by messages with attachments

[AMBER] significance of iwrap Saikat Pal (Fri Sep 01 2017 - 04:59:28 PDT)
1. 1wrap_1.png (225688 bytes)
2. iwrap_0.png (254191 bytes)
[AMBER] Moldeling with MCPB.py Lê Ngọc Chính (Mon Sep 04 2017 - 04:09:45 PDT)
1. HIC.frcmod (388 bytes)
2. CU.mol2 (281 bytes)
3. 4opb.pdb (443636 bytes)
4. HIC.mol2 (2468 bytes)
5. 4opb_fix1.pdb (277668 bytes)
6. CU.in (194 bytes)
[AMBER] Residue wise energy decomposition via MM-PBSA Rajarshi Roy (Mon Sep 04 2017 - 21:06:49 PDT)
1. 09-05_09-13-28.png (367390 bytes)
2. FINAL_DECOMP_MMPBSA.dat (184929 bytes)
[AMBER] Error after using Parmed: A residue defined as "fast 3-point water"... David Sáez (Thu Sep 07 2017 - 16:07:32 PDT)
1. psfscript.psf (446 bytes)
[AMBER] Frcmod file for ionic liquids guptashilpa_91.yahoo.com (Fri Sep 08 2017 - 07:42:13 PDT)
1. frcmod.bf4 (277 bytes)
2. acn.pdb (410 bytes)
3. bf4.pdb (343 bytes)
4. bmi.pdb (1683 bytes)
5. bmi.pdb (2651 bytes)
Re: [AMBER] umbrella sampling - restraint problem Nisha Amarnath Jonniya (Fri Sep 08 2017 - 07:57:10 PDT)
1. disang1.rst (322 bytes)
[AMBER] Frcmod file for ionic liquids Shilpa Gupta (Fri Sep 08 2017 - 21:43:05 PDT)
1. frcmod.bf4 (277 bytes)
2. acn.pdb (410 bytes)
3. bf4.pdb (343 bytes)
4. bmi.mol2 (2651 bytes)
5. bmi.pdb (1683 bytes)
Re: [AMBER] Error in quasiharmonic calculation: prmtop file? Nada Afiva (Sat Sep 09 2017 - 20:55:07 PDT)
1. _MMPBSA_cpptraj_entropy.out (4309 bytes)
[AMBER] index error -reg Jeyaram R A (Sun Sep 10 2017 - 04:54:00 PDT)
1. protein_screenshot_.jpg (106639 bytes)
2. reduce_info.log (44481 bytes)
[AMBER] CNT hongping zhang (Sun Sep 10 2017 - 18:58:34 PDT)
1. SWNT__2_.pdb (8065 bytes)
Re: [AMBER] umbrella sampling - restraint problem Nisha Amarnath Jonniya (Sun Sep 10 2017 - 22:21:44 PDT)
1. disang2.rst (972 bytes)
[AMBER] How to use two different force fields for a molecule? Anhui Wang (Mon Sep 11 2017 - 07:09:05 PDT)
1. beta-CD.png (16480 bytes)
Re: [AMBER] tleap atom numbering Neha Gandhi (Mon Sep 11 2017 - 14:38:23 PDT)
1. frcmod.cnt (277 bytes)
2. cnt.mol2 (166277 bytes)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Tue Sep 12 2017 - 02:07:28 PDT)
1. IMG_0043.jpg (199957 bytes)
Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe (Tue Sep 12 2017 - 05:05:32 PDT)
1. 12092017_Zn_site.jpg (42427 bytes)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Tue Sep 12 2017 - 05:31:26 PDT)
1. IMG_0043.jpg (199957 bytes)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Tue Sep 12 2017 - 05:39:23 PDT)
1. 09-12_______8.36.14.png (119123 bytes)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Tue Sep 12 2017 - 05:54:12 PDT)
1. 09-12_______8.52.50.png (207750 bytes)
[AMBER] Creation of unusual bonding via pdb4amber. Rajarshi Roy (Tue Sep 12 2017 - 11:18:18 PDT)
1. peptide.pdb (7845 bytes)
2. peptide_clean.pdb (7321 bytes)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Tue Sep 12 2017 - 18:52:04 PDT)
1. IMG_0044.jpg (487682 bytes)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Tue Sep 12 2017 - 19:45:30 PDT)
1. 09-13_______10.43.26.png (118347 bytes)
Re: [AMBER] Creation of unusual bonding via pdb4amber. Rajarshi Roy (Tue Sep 12 2017 - 22:52:43 PDT)
1. leap.log (9566 bytes)
[AMBER] Total energy of peptide simulation is positive Chetna Tyagi (Thu Sep 14 2017 - 05:51:00 PDT)
1. image.png (56297 bytes)
2. image.png (60859 bytes)
[AMBER] Mcpb.py for bay60 compound Rana Rehan Khalid (Sat Sep 16 2017 - 10:43:17 PDT)
1. 4iae.pdb (168028 bytes)
2. 1DX.frcmod (764 bytes)
3. 1DX.mol2 (8304 bytes)
4. 1DX.pdb (3555 bytes)
Re: [AMBER] MCPB.py hbay.in input (system does not have metal ion) Rana Rehan Khalid (Sat Sep 16 2017 - 23:58:25 PDT)
1. 4iae.pdb (160788 bytes)
Re: [AMBER] Manually set residues Protonation states for HIS and CYS Rana Rehan Khalid (Sun Sep 17 2017 - 12:30:16 PDT)
1. 4iae.pdb (160788 bytes)
Re: [AMBER] Error in MM-PBSA -- BondError: Cannot exclude an atom from itself 康宁 (Sun Sep 17 2017 - 18:47:37 PDT)
1. Mg.prmtop (11103 bytes)
[AMBER] Problem with parallel install Maria Clelia Milletti (Mon Sep 18 2017 - 09:18:47 PDT)
1. config.log (480862 bytes)
Re: [AMBER] Problem with parallel install Maria Clelia Milletti (Tue Sep 19 2017 - 07:35:58 PDT)
1. 09-18_18-38-18.diff (1569 bytes)
2. 09-18_18-38-18.log (669695 bytes)
[AMBER] Antechamber Rana Rehan Khalid (Wed Sep 20 2017 - 09:46:19 PDT)
1. 1DX.frcmod (764 bytes)
Re: [AMBER] Problem with parallel install Maria Clelia Milletti (Wed Sep 20 2017 - 13:13:55 PDT)
1. test.out (5806 bytes)
Re: [AMBER] Problem with parallel install Maria Clelia Milletti (Wed Sep 20 2017 - 13:54:28 PDT)
1. 09-18_18-38-18.diff (1569 bytes)
2. 09-18_18-38-18.log (669695 bytes)
Re: [AMBER] Problem with parallel install Maria Clelia Milletti (Thu Sep 21 2017 - 06:54:18 PDT)
1. config.log (480824 bytes)
Re: [AMBER] Antechamber error Rana Rehan Khalid (Thu Sep 21 2017 - 09:03:28 PDT)
1. 1DX_h.pdb (6258 bytes)
Re: [AMBER] Pytraj Gyration Tensor Daniel Roe (Thu Sep 21 2017 - 12:35:56 PDT)
1. test.out (2521 bytes)
2. radgyr.tensor.dat (1078 bytes)
Re: [AMBER] SHAKE failure Lizelle Lubbe (Fri Sep 22 2017 - 11:37:05 PDT)
1. eq2_frame_1.jpg (141525 bytes)
2. eq2_frame_40.jpg (140907 bytes)
3. eq2_frame_29.jpg (140787 bytes)
4. eq2_frame_20.jpg (145803 bytes)
[AMBER] Antechamber RESP calculation error Rana Rehan Khalid (Sat Sep 23 2017 - 10:05:26 PDT)
1. bay_before_opt.png (163764 bytes)
2. bay_after_opt.png (158376 bytes)
Re: [AMBER] cluster analysis using cpptraj Sowmya Indrakumar (Mon Sep 25 2017 - 02:47:51 PDT)
1. 09-25_11-45-00.png (67315 bytes)
[AMBER] Problem in analysing radius of gyration value in CPPTRAJ krishna.2015.iitg.ernet.in (Tue Sep 26 2017 - 09:07:04 PDT)
1. Untitled.ps (277685 bytes)
2. rmsd_protein.in (239 bytes)
3. radgyr_protein.in (203 bytes)
[AMBER] [Fwd: Re: Problem in analysing radius of gyration value in CPPTRAJ] krishna.2015.iitg.ernet.in (Wed Sep 27 2017 - 11:35:23 PDT)
1. VMD_Timeline_Window_initial.eps (76484 bytes)
2. VMD_Timeline_Window_8250.zip (164170 bytes)
Re: [AMBER] Problem in analysing radius of gyration value in CPPTRAJ krishna.2015.iitg.ernet.in (Thu Sep 28 2017 - 04:01:40 PDT)
1. VMD_Timeline_Window_initial.eps (76484 bytes)
2. 1.jpg (170024 bytes)

Amber Archive Sep 2017 by messages with attachments