Amber Archive Apr 2012 by messages with attachments

Re: [AMBER] error in making prmtop & inpcrd for ligand-protein complex Aditya Setiajid (Mon Apr 02 2012 - 19:32:03 PDT)
1. 6COXS.pdb (363465 bytes)
2. log_tleap.txt.txt (4836 bytes)
[AMBER] "Possible Failures" in Amber 11 and Amber tools tests Dureid El-Moghraby (Tue Apr 03 2012 - 03:27:49 PDT)
1. logs_and_diffs.tar.gz (230698 bytes)
[AMBER] Inconsistent Internal energy from monomer to dimer Josep Maria Campanera Alsina (Tue Apr 03 2012 - 04:15:55 PDT)
1. monomer.pdb (27341 bytes)
2. monomer.top (175680 bytes)
3. dimer.pdb (54699 bytes)
4. dimer.top (334911 bytes)
5. monomer_mmgbsa_perl_statistics.out (386 bytes)
6. dimer_mmgbsa_perl_statistics.out (386 bytes)
7. mmgbsa_python_statistics.out (5640 bytes)
8. dimer.md_24.o.zip (81701 bytes)
9. monomer.md_51.o.zip (79714 bytes)
Re: [AMBER] Inconsistent Internal energy from monomer to dimer Josep Maria Campanera Alsina (Wed Apr 04 2012 - 00:40:56 PDT)
1. mmgbsa_python_statistics.out (5640 bytes)
Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss (Wed Apr 04 2012 - 05:39:04 PDT)
1. md3.out.gz (55915 bytes)
2. md1.out.gz (52872 bytes)
Re: [AMBER] Could not read velocities from restart file Ross Walker (Tue Apr 10 2012 - 13:59:26 PDT)
1. inpcrd.rst.gz (682662 bytes)
2. prmtop.gz (279956 bytes)
3. mdin (244 bytes)
Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss (Wed Apr 04 2012 - 05:34:52 PDT)
1. md1.out (475180 bytes)
2. md3.out (475113 bytes)
[AMBER] Residue mismatch - Amber11 sławek bojarowski (Tue Apr 10 2012 - 14:47:18 PDT)
1. mmpbsa.in (238 bytes)
2. b.prmtop (13182 bytes)
3. a.prmtop (13182 bytes)
4. ab.prmtop (17132 bytes)
Re: [AMBER] Could not read velocities from restart file Ross Walker (Tue Apr 10 2012 - 15:49:33 PDT)
1. 2012_04_10_restrt_patch.dat (1074 bytes)
[AMBER] Error: Could not parse GB output files! Check for missing values (*********). zhangaidi (Wed Apr 11 2012 - 07:24:50 PDT)
1. files.rar (3641 bytes)
[AMBER] Error: Could not parse GB output files! Check for missing values (*********). zhangaidi (Wed Apr 11 2012 - 07:35:40 PDT)
1. mmpbsa_per_res_decomp.in (214 bytes)
2. progress.log (1741 bytes)
3. _MMPBSA_complex_pb.mdout (18970 bytes)
Re: [AMBER] parameters for Lys-sugar P2N file Urszula Uciechowska (Wed Apr 11 2012 - 09:33:52 PDT)
1. out.p2n (39229 bytes)
2. out.pdb (32732 bytes)
3. Mol_red1.pdb (16753 bytes)
[AMBER] parameters for Lys-sugar P2N file Urszula Uciechowska (Thu Apr 12 2012 - 01:48:53 PDT)
1. out.p2n (39229 bytes)
2. out.pdb (32732 bytes)
3. Mol_red1.pdb (16753 bytes)
[AMBER] Query regarding Amber 11 Somnath Nandy (Thu Apr 12 2012 - 05:39:42 PDT)
1. image001.jpg (7023 bytes)
2. image002.jpg (1665 bytes)
Re: [AMBER] MMPBSA error in segmentation fault Aditya Setiajid (Fri Apr 13 2012 - 23:03:28 PDT)
1. _MMPBSA_receptor_gb.mdout (1016 bytes)
2. MMPBSA.log (819 bytes)
Re: [AMBER] [amber] error: could not parse gb output files! check for missing values (*********). zhangaidi (Sat Apr 14 2012 - 04:57:24 PDT)
1. _MMPBSA_receptor_pb.mdout (17140 bytes)
2. _MMPBSA_ligand_pb.mdout (9820 bytes)
3. _MMPBSA_complex_pb.mdout (18970 bytes)
Re: [AMBER] abertools12 installation failure Jason Swails (Sun Apr 15 2012 - 08:22:21 PDT)
1. configure.patch (688 bytes)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Mon Apr 16 2012 - 06:47:57 PDT)
1. ESP_pb1.in (104 bytes)
2. ESP_pb1.out (29440 bytes)
3. ESP_pb.in (173 bytes)
4. ESP_pb.out (21534 bytes)
5. ESP_test1.inpcrd (3330 bytes)
6. ESP_test1.prmtop (47401 bytes)
[AMBER] Error while running mm_pbsa.pl Prashant Kumar (Mon Apr 16 2012 - 08:30:14 PDT)
1. Water_OH-pi.tar.gz (14105 bytes)
2. Uracil_BP.tar.gz (20951 bytes)
Re: [AMBER] saveamberparm in xleap does not recognize atom type F Genzo Tanaka (Mon Apr 16 2012 - 09:13:13 PDT)
1. last.log (4378 bytes)
[AMBER] AmberTools12 Installation Error Senthil Natesan (Mon Apr 16 2012 - 12:59:20 PDT)
1. ambertools12_installation_error.txt (36447 bytes)
Re: [AMBER] MMPBSA error Jan-Philip Gehrcke (Tue Apr 17 2012 - 05:28:02 PDT)
1. findprogs.diff (1187 bytes)
2. MMPBSA.diff (543 bytes)
Re: [AMBER] MMPBSA error Jan-Philip Gehrcke (Tue Apr 17 2012 - 05:40:58 PDT)
1. MMPBSA.diff (680 bytes)
[AMBER] P2N file error from RED Urszula Uciechowska (Tue Apr 17 2012 - 05:59:11 PDT)
1. Mol_red1.p2n (32081 bytes)
Re: [AMBER] :Re: "closest" command in cpptraj Daniel Roe (Tue Apr 17 2012 - 08:05:00 PDT)
1. Action_Closest.patch (4162 bytes)
[AMBER] Using Antechamber to generate RESP prepi file Lianhu Wei (Tue Apr 17 2012 - 14:12:29 PDT)
1. KP92_Esp_Low.log (608407 bytes)
[AMBER] Why RMSD goes fast to 5 angstrom? Shulin Zhuang (Tue Apr 17 2012 - 19:26:20 PDT)
1. figure.jpg (119614 bytes)
Re: [AMBER] Using Antechamber to generate RESP prepi file Lianhu Wei (Wed Apr 18 2012 - 12:27:42 PDT)
1. KP92_Low_RESP.crg (334 bytes)
2. KP92_Esp_Low_espgen.esp (396776 bytes)
3. KP92_Esp_Low_respgen.respin (576 bytes)
4. KP92_Low_RESP.ac (3709 bytes)
Re: [AMBER] why no periodic information? Albert (Wed Apr 18 2012 - 12:29:01 PDT)
1. Screenshot.png (16054 bytes)
Re: [AMBER] why no periodic information? Albert (Wed Apr 18 2012 - 12:29:20 PDT)
1. Screenshot.png (16054 bytes)
[AMBER] Bug? Antechamber, Ambertools-1.4 Lianhu Wei (Thu Apr 19 2012 - 13:11:46 PDT)
1. Kp92_Comp01.bz2 (336114 bytes)
2. Kp92_Comp02.bz2 (426707 bytes)
[AMBER] The error of installing mpi4py in ambertools12 for MMPBSA parallel JiYuan Liu (Fri Apr 20 2012 - 21:13:02 PDT)
1. mpi4py_install.log (2614 bytes)
[AMBER] Confusion in adding TER cards Asmita Gupta (Fri Apr 20 2012 - 04:05:24 PDT)
1. test.pdb (118426 bytes)
Re: [AMBER] cpptraj, ptraj and time interval Jan-Philip Gehrcke (Fri Apr 20 2012 - 08:15:04 PDT)
1. ptrajrms_convert_frame_to_time.py (1576 bytes)
[AMBER] error in AMBER while generatting prmtop and ipcrd kureeckal ramesh (Mon Apr 23 2012 - 01:56:11 PDT)
1. 1A4H_gelda.pdb (144340 bytes)
2. gelda_opt.pdb (5360 bytes)
3. error_1.txt (2820 bytes)
4. error_2.txt (759 bytes)
Re: [AMBER] parameters for Lys-sugar Urszula Uciechowska (Mon Apr 23 2012 - 03:38:24 PDT)
1. o3-sm.mol2 (4761 bytes)
[AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration Marek Maly (Mon Apr 23 2012 - 09:55:26 PDT)
1. GeneralScripts.zip (93742 bytes)
Re: [AMBER] AMBER12 build on Linux x86_64 Shaw, Sharon (Mon Apr 23 2012 - 13:51:14 PDT)
1. make.install.out.gz (139921 bytes)
[AMBER] AMBER 11 sander segmentation fault Shuyi Cao (Mon Apr 23 2012 - 16:32:21 PDT)
1. 3e9s_methyl_F2124_0890_2.pdb (201371 bytes)
2. tleap_1.in (742 bytes)
3. tleap.in (300 bytes)
4. min1.in (175 bytes)
Re: [AMBER] parameters for Lys-sugar leap errors Urszula Uciechowska (Thu Apr 26 2012 - 02:41:01 PDT)
1. MGR.off (6356 bytes)
2. MGR.pdb (10036 bytes)
[AMBER] Problem with molegro file Chris Chris (Fri Apr 27 2012 - 09:52:31 PDT)
1. CTZ_5_xleap.pdb (3693 bytes)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Sat Apr 28 2012 - 05:13:08 PDT)
1. 1VJ5.rst (6542 bytes)
2. 1VJ5.top (82045 bytes)
3. 1VJ5pbsa.phi (275890 bytes)

Last message date: Mon Apr 30 2012 - 21:00:02 PDT
Archived on: Mon Dec 23 2024 - 05:54:28 PST

834 messages sort by: [ thread ] [ author ] [ date ] [ subject ] [ attachment ]

Custom Search