Amber Archive May 2010 by messages with attachments

Re: [AMBER] ambertools 1.4, tests Ben Roberts (Mon May 03 2010 - 07:53:26 PDT)
1. 05-03_09-55-20.diff (7904 bytes)
[AMBER] How to make ionic liquid solvent box? 김호신 (Mon May 03 2010 - 12:24:34 PDT)
1. emimtfo.mol2 (3602 bytes)
Re: [AMBER] nmr order parameter and autocorrelation Samuel Genheden (Mon May 03 2010 - 21:59:53 PDT)
1. mat2s2.py (1528 bytes)
Re: [AMBER] problem on running saveAmberParm tianyuan meng (Tue May 04 2010 - 02:20:26 PDT)
1. wt1mg_water.pdb (130968 bytes)
RE: [AMBER] How to make ionic liquid solvent box? 킹아기돼지 (Tue May 04 2010 - 13:42:20 PDT)
1. emim.mol2 (2650 bytes)
2. tfo.mol2 (1336 bytes)
3. result.mol2 (5788 bytes)
RE: [AMBER] How to make ionic liquid solvent box? Hoshin Kim (Tue May 04 2010 - 14:06:39 PDT)
1. emim.mol2 (2650 bytes)
2. tfo.mol2 (1336 bytes)
3. result.mol2 (5788 bytes)
Re: [AMBER] How to make ionic liquid solvent box? Hoshin Kim (Tue May 04 2010 - 15:41:56 PDT)
1. tfo.mol2 (1336 bytes)
2. emim.mol2 (2650 bytes)
3. result.mol2 (5788 bytes)
[AMBER] MM-PBSA problem.. large delta (PBTOT, GAS, VdW, INT) Matthias Negri (Wed May 05 2010 - 03:17:45 PDT)
1. 6500.zip (569653 bytes)
2. m_negri.vcf (376 bytes)
[AMBER] [Fwd: MM-PBSA problem.. large delta (PBTOT, GAS, VdW, INT)] Matthias Negri (Wed May 05 2010 - 03:47:24 PDT)
1. 6500.tgz (573672 bytes)
2. m_negri.vcf (376 bytes)
[AMBER] NaNs in wham analysis Lekpa Duukori (Wed May 05 2010 - 11:37:15 PDT)
1. timeseries.png (28706 bytes)
Re: [AMBER] NaNs in wham analysis Lekpa Duukori (Wed May 05 2010 - 12:32:33 PDT)
1. zeta.dat (525000 bytes)
Re: [AMBER] MM-PBSA problem.. large delta (PBTOT, GAS, VdW, INT) Matthias Negri (Wed May 05 2010 - 16:45:29 PDT)
1. m_negri.vcf (376 bytes)
[AMBER] unsubscribe Cojocaru,Vlad (Thu May 06 2010 - 01:12:19 PDT)
1. winmail.dat (0 bytes)
[AMBER] can't make proper use of IGB flag, it cause "input conversion error" geyan (Thu May 06 2010 - 01:30:43 PDT)
1. min.in (249 bytes)
2. heat.in (261 bytes)
3. density.in (254 bytes)
4. equil.in (179 bytes)
5. every_500ps_product.in (229 bytes)
Re: [AMBER] MM-PBSA problem.. large delta (PBTOT, GAS, VdW, INT) Matthias Negri (Thu May 06 2010 - 13:11:55 PDT)
1. m_negri.vcf (376 bytes)
Re: [AMBER] MM-PBSA problem.. large delta (PBTOT, GAS, VdW, INT) Matthias Negri (Thu May 06 2010 - 15:29:12 PDT)
1. m_negri.vcf (376 bytes)
[AMBER] (no subject) Waad RHAIEM (Sun May 09 2010 - 17:13:58 PDT)
1. Amber_8_serial_calculation.doc (98304 bytes)
2. Amber_8_parallel_version.doc (74240 bytes)
[AMBER] simulations RAMD on serial and parallel version of amber8 Waad RHAIEM (Sun May 09 2010 - 17:17:59 PDT)
1. Amber_8_serial_calculation.doc (98304 bytes)
2. Amber_8_parallel_version.doc (74240 bytes)
[AMBER] [Fwd: problem in bond connection] RINU KHATTRI (Tue May 11 2010 - 05:43:42 PDT)
1. target_1.pdb (72643 bytes)
[AMBER] PMEMD installation with gfortran Senthil Natesan (Tue May 11 2010 - 15:13:46 PDT)
1. pmemd_installation_error.txt (10699 bytes)
Re: [AMBER] PMEMD installation with gfortran Senthil Natesan (Wed May 12 2010 - 06:58:11 PDT)
1. error2.txt (12328 bytes)
[AMBER] Ptraj image problems Jayalakshmi Sridhar (Wed May 12 2010 - 11:26:26 PDT)
1. jsridhar.vcf (205 bytes)
Re: [AMBER] Ptraj image problems Jayalakshmi Sridhar (Wed May 12 2010 - 12:18:35 PDT)
1. jsridhar.vcf (205 bytes)
Re: [AMBER] Ptraj image problems Jayalakshmi Sridhar (Wed May 12 2010 - 12:56:42 PDT)
1. vmd_ptrajimage.jpg (84305 bytes)
2. jsridhar.vcf (205 bytes)
Re: [AMBER] Ptraj image problems Jayalakshmi Sridhar (Wed May 12 2010 - 13:07:28 PDT)
1. jsridhar.vcf (205 bytes)
Re: [AMBER] Ptraj image problems Jayalakshmi Sridhar (Wed May 12 2010 - 13:19:22 PDT)
1. jsridhar.vcf (205 bytes)
Re: [AMBER] Ptraj image problems Jayalakshmi Sridhar (Wed May 12 2010 - 13:23:10 PDT)
1. jsridhar.vcf (205 bytes)
Re: [AMBER] pressure not constant ashutosh shandilya (Thu May 13 2010 - 00:08:03 PDT)
1. DENSITY___v.doc (33280 bytes)
Re: [AMBER] Ptraj image problems Jayalakshmi Sridhar (Thu May 13 2010 - 08:40:00 PDT)
1. jsridhar.vcf (205 bytes)
Re: [AMBER] Ptraj image problems Jayalakshmi Sridhar (Thu May 13 2010 - 08:40:50 PDT)
1. jsridhar.vcf (205 bytes)
[AMBER] problem with targeted md simulation map110.pitt.edu (Thu May 13 2010 - 12:19:36 PDT)
1. targetedmd.tar.bz2 (1427005 bytes)
Re: [AMBER] problem with targeted md simulation map110.pitt.edu (Thu May 13 2010 - 13:30:24 PDT)
1. ptraj.tar.bz2 (92933 bytes)
Re: [AMBER] problem with targeted md simulation map110.pitt.edu (Fri May 14 2010 - 08:05:45 PDT)
1. frame0.pdb (93721 bytes)
2. ptraj.out (1901 bytes)
Re: [AMBER] color images from 2drms InSuk Joung (Fri May 14 2010 - 09:49:07 PDT)
1. plot_2drms.pl (2199 bytes)
[AMBER] solvent MD - poor equilibration Senthil Natesan (Fri May 14 2010 - 12:31:48 PDT)
1. md1.out (124133 bytes)
[AMBER] problems enabling CUDA for Amber 11 on Mac OS X 10.6 Steve Constable (Fri May 14 2010 - 13:16:58 PDT)
1. configure (52723 bytes)
Re: [AMBER] regarding H-bond & torsion angles shamoon siddiqui (Fri May 14 2010 - 22:37:46 PDT)
1. analyse_hbond.ptraj (2702 bytes)
Re: [AMBER] installation on MacOS10.6 erik zuiderweg (Sat May 15 2010 - 14:19:33 PDT)
1. error_install_gcc44 (3080 bytes)
PROGRESS! [AMBER] installation on MacOS10.6 erik zuiderweg (Sun May 16 2010 - 12:27:10 PDT)
1. make_log (20982 bytes)
Re: [AMBER] QMMM and Thermodynamic integration InSuk Joung (Mon May 17 2010 - 11:50:20 PDT)
1. qmmm_ti.tar.gz (42142 bytes)
Re: [AMBER] solvent MD - poor equilibration Senthil Natesan (Mon May 17 2010 - 12:12:07 PDT)
1. complex.png (161855 bytes)
2. density.png (12931 bytes)
3. energy.png (10141 bytes)
4. pressure.png (18222 bytes)
5. temp.png (17579 bytes)
6. volume.png (14212 bytes)
Re: [AMBER] solvent MD - poor equilibration Senthil Natesan (Mon May 17 2010 - 13:14:59 PDT)
1. density.png (12931 bytes)
Re: PROGRESS! [AMBER] installation on MacOS10.6 erik zuiderweg (Mon May 17 2010 - 15:35:11 PDT)
1. 05-17_17-45-38.log (82826 bytes)
2. 05-17_17-04-43.log (57765 bytes)
Re: [AMBER] solvent MD - poor equilibration Senthil Natesan (Tue May 18 2010 - 07:17:03 PDT)
1. volume.png (14212 bytes)
2. density.png (12931 bytes)
[AMBER] AT1.4 installation errors (logs are attached) Dmitry Mukha (Tue May 18 2010 - 08:19:13 PDT)
1. config.h (3644 bytes)
2. fftw2_config.log (5135 bytes)
3. netcdf_config.log (10689 bytes)
4. install.log (301976 bytes)
Re: [AMBER] Installation of Amber10 jaya c.jose (Tue May 18 2010 - 08:20:56 PDT)
1. config.h (1137 bytes)
RE: [AMBER] Installation of Amber10 Ross Walker (Tue May 18 2010 - 08:34:27 PDT)
1. config.h (951 bytes)
[AMBER] Positive Etot value Hoshin Amber (Tue May 18 2010 - 19:55:54 PDT)
1. min.in (379 bytes)
2. eq2.in (391 bytes)
3. eq1.in (570 bytes)
Re: [AMBER] AMBER10 installation on OSX erik zuiderweg (Thu May 20 2010 - 07:53:12 PDT)
1. INSTALLING_AMBER (3036 bytes)
[AMBER] NMR distance restraints read but not used Douglas Kojetin (Fri May 21 2010 - 10:40:15 PDT)
1. example.out (16696 bytes)
Re: [AMBER] leap issues Alex Boncheff (Fri May 21 2010 - 10:43:09 PDT)
1. y.prep (2328 bytes)
[AMBER] help about test failures peker milas (Fri May 21 2010 - 13:32:34 PDT)
1. TEST_FAILURES_MM.txt (35203 bytes)
Re: [AMBER] AT1.4 installation errors (logs are attached) Mengjuei Hsieh (Fri May 21 2010 - 22:49:18 PDT)
1. debug01.txt (1222 bytes)
[AMBER] (no subject) Nicee (Mon May 24 2010 - 02:54:01 PDT)
1. new7_mtb3_tleap.pdb (347206 bytes)
2. new7_mtb3_min12_pdb.pdb (347206 bytes)
[AMBER] Atom out of bounds/prepin file problem Nicee (Mon May 24 2010 - 02:55:48 PDT)
1. new7_mtb3_tleap.pdb (347206 bytes)
2. new7_mtb3_min12_pdb.pdb (347206 bytes)
Re: [AMBER] TI Job crashes at some lambda values during heating sunita gupta (Mon May 24 2010 - 03:14:43 PDT)
1. amberrun_vdw.sh (5308 bytes)
[AMBER] radius of gyration in ptraj Jayalakshmi Sridhar (Mon May 24 2010 - 11:30:06 PDT)
1. jsridhar.vcf (205 bytes)
[AMBER] Problem about Sander with large system Tom Williams (Mon May 24 2010 - 19:58:53 PDT)
1. Project_XY.jpg (25858 bytes)
2. Project_XZ.jpg (34164 bytes)
[AMBER] AMBER Asfa Ali (Mon May 24 2010 - 22:40:35 PDT)
1. 1kf1_w.pdb (37862 bytes)
2. 1kf1__w_md2.pdb.1000 (49950 bytes)
[AMBER] regarding MMPBSA Asfa Ali (Tue May 25 2010 - 03:15:05 PDT)
1. mmpbsa.in (129 bytes)
[AMBER] antechamber missing_grace.sina.com (Tue May 25 2010 - 21:57:27 PDT)
1. 1G5Q.gjf (4092 bytes)
2. 1G5Q.pdb (3402 bytes)
[AMBER] amber missing_grace.sina.com (Tue May 25 2010 - 21:59:02 PDT)
1. 1G5Q.gjf (4092 bytes)
2. 1G5Q.pdb (3402 bytes)
Re: [AMBER] amber Levi Pierce (Tue May 25 2010 - 22:24:37 PDT)
1. log_to_pdb.awk (4264 bytes)
[AMBER] B-DNA monica.imtech.res.in (Wed May 26 2010 - 04:18:02 PDT)
1. nuc.in (364 bytes)
[AMBER] Energy minimization OR black art M. Reza Ganjalikhany (Wed May 26 2010 - 05:41:45 PDT)
1. GYR.jpg (59062 bytes)
2. rmsd_Ca.jpg (61373 bytes)
3. rmsf_CA.jpg (41953 bytes)
Re: [AMBER] amber11 PMEMD cuda problem. (sometimes stopped...) Wookyung Yu (Thu May 27 2010 - 21:57:51 PDT)
1. send.tar.gz (1130190 bytes)
Re: [AMBER] installing AmberTools 1.4 on AIX case (Sat May 29 2010 - 19:32:42 PDT)
1. sqm_aix.patch (1631 bytes)
Re: [AMBER] MMPBSA.py update install problem Bill Miller III (Sun May 30 2010 - 17:44:09 PDT)
1. MMPBSA_Python_Manual.pdf (124915 bytes)
Re: [AMBER] MMPBSA.py update install problem Jason Swails (Mon May 31 2010 - 06:07:49 PDT)
1. mmpbsa.patch (1810 bytes)

Last message date: Tue Jun 01 2010 - 00:00:03 PDT
Archived on: Fri Nov 15 2024 - 05:54:07 PST

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