Amber Archive Jul 2011 by messages with attachments

[AMBER] INSTALLATION ERROR ON RED HAT LINUX Rajabrata Bhuyan (Thu Jun 30 2011 - 23:13:28 PDT)
1. amber_failure (15149 bytes)
Re: [AMBER] dist restraint e p (Fri Jul 01 2011 - 22:03:00 PDT)
1. mdout (8498 bytes)
[AMBER] dist restraint e p (Fri Jul 01 2011 - 22:05:30 PDT)
1. mdout (8498 bytes)
Re: [AMBER] Error mmpbsa John S (Fri Jul 01 2011 - 22:15:14 PDT)
1. pbsa.out (79584 bytes)
[AMBER] DNA simulation najmul arfin (Sun Jul 03 2011 - 22:55:38 PDT)
1. md1.in (373 bytes)
2. md2.in (288 bytes)
3. mix_min1.in (143 bytes)
4. mix_min2.in (198 bytes)
5. xleap.log (114476 bytes)
[AMBER] using sleap to load mol2 files case (Mon Jul 04 2011 - 06:15:03 PDT)
1. mol2.bugfix (2992 bytes)
Re: [AMBER] regarding per residue wise free energy decomposition Hirdesh Kumar (Mon Jul 04 2011 - 22:26:05 PDT)
1. test.log (3581 bytes)
[AMBER] Large flcutions in the RMSD deviations upon changing the parameters values of gamma_ln, taup and timesteps ..How a small variation leads to such a larage change?? Rajesh Raju (Tue Jul 05 2011 - 16:27:58 PDT)
1. rmsd1.jpeg (308414 bytes)
2. RMSD.pdf (212314 bytes)
[AMBER] AmberTools installation - Jennifer L. Muzyka (Wed Jul 06 2011 - 05:18:28 PDT)
1. 07-06_07-55-39.log (46062 bytes)
2. 07-06_07-55-39.diff (1353 bytes)
[AMBER] Different trajectories with large difference in RMSD with changing the parameters values of gamma_ln, taup, timesteps and extend of density equilibration Rajesh Raju (Wed Jul 06 2011 - 08:59:32 PDT)
1. rmsd1.jpeg (308414 bytes)
2. RMSD.pdf (212314 bytes)
Re: [AMBER] sander job crashed Ben Roberts (Thu Jul 07 2011 - 17:02:30 PDT)
1. smime.p7s (2670 bytes)
Re: [AMBER] sander job crashed Ben Roberts (Fri Jul 08 2011 - 04:59:23 PDT)
1. smime.p7s (3919 bytes)
[AMBER] XLEaP parameters for nonstandard residues Julia Blum (Fri Jul 08 2011 - 07:05:51 PDT)
1. edit.mol2 (8371 bytes)
2. edit.frcmod (410 bytes)
3. c-pf.pdb (50593 bytes)
Re: [AMBER] XLEaP parameters for nonstandard residues Julia Blum (Fri Jul 08 2011 - 09:26:04 PDT)
1. edit.mol2 (8371 bytes)
2. edit.frcmod (410 bytes)
Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration Rajesh Raju (Fri Jul 08 2011 - 13:16:48 PDT)
1. rmsd.jpeg (307044 bytes)
2. RMSD.pdf (212314 bytes)
Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration Rajesh Raju (Fri Jul 08 2011 - 14:00:07 PDT)
1. RMSD.pdf (212314 bytes)
Re: [AMBER] sander job crashed Ben Roberts (Mon Jul 11 2011 - 08:24:21 PDT)
1. smime.p7s (3919 bytes)
Re: [AMBER] cudaMemcpy GpuBuffer::Upload failed invalid argument Oliver Kuhn (Mon Jul 11 2011 - 10:24:45 PDT)
1. s01.tar.gzip (963273 bytes)
Re: [AMBER] Ala double mutation scans Dwight McGee (Mon Jul 11 2011 - 10:36:58 PDT)
1. make_crd.in (283 bytes)
[AMBER] help xiao fugui (Mon Jul 11 2011 - 19:16:56 PDT)
1. part (5950 bytes)
2. part (33302 bytes)
3. part (32379 bytes)
4. part (222421 bytes)
[AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Tue Jul 12 2011 - 07:59:28 PDT)
1. sqm.out (8190 bytes)
Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Tue Jul 12 2011 - 09:37:15 PDT)
1. 7_12_3F5O_chemdraw3.pdb (11920 bytes)
Re: [AMBER] zinc parameters Ben Roberts (Tue Jul 12 2011 - 10:11:01 PDT)
1. smime.p7s (2670 bytes)
Re: [AMBER] problem with type of pdb output. Ben Roberts (Tue Jul 12 2011 - 11:51:50 PDT)
1. smime.p7s (2670 bytes)
Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Tue Jul 12 2011 - 12:40:39 PDT)
1. coh1.pdb (8932 bytes)
[AMBER] the picture of secstruct and the analysis of Hbond qiao xue (Tue Jul 12 2011 - 18:57:54 PDT)
1. secstruct.jpg (4792 bytes)
2. Hbond.jpg (8902 bytes)
Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Wed Jul 13 2011 - 07:28:45 PDT)
1. 1.pdb (6777 bytes)
Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Wed Jul 13 2011 - 07:53:48 PDT)
1. 1.pdb (6777 bytes)
2. coh1.pdb (8932 bytes)
Re: [AMBER] Antechamber trouble with COA-acyl chain intra\\sa175950 (Wed Jul 13 2011 - 08:30:20 PDT)
1. 1b_good.pdb (6679 bytes)
[AMBER] TR: Antechamber trouble with COA-acyl chain intra\\sa175950 (Wed Jul 13 2011 - 08:34:36 PDT)
1. 1b_good.pdb (6679 bytes)
2. ATT00049.txt (134 bytes)
Re: [AMBER-Developers] [AMBER] Antechamber trouble with COA-acyl chain David A Case (Wed Jul 13 2011 - 11:10:44 PDT)
1. sqm.in (5381 bytes)
2. sqm_g09.in (5175 bytes)
Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Wed Jul 13 2011 - 12:59:03 PDT)
1. 1_sqmGAUS.pdb (6681 bytes)
Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Wed Jul 13 2011 - 13:10:42 PDT)
1. 1_sqmGAUS.mol2 (9824 bytes)
[AMBER] How to make the picture of secstruct and the analysis of Hbond qiao xue (Wed Jul 13 2011 - 16:54:10 PDT)
1. secstruct.jpg (4792 bytes)
2. Hbond.jpg (8902 bytes)
Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Thu Jul 14 2011 - 07:07:46 PDT)
1. hco.mol2 (9823 bytes)
Re: [AMBER] How to make the picture of secstruct and the analysis of Hbond qiao xue (Fri Jul 15 2011 - 20:21:04 PDT)
1. hbond.ptraj (1594 bytes)
2. hbond.out (7558 bytes)
Re: [AMBER] nonbond parameter for copper(Ⅱ) ion Marek Maly (Sat Jul 16 2011 - 14:47:54 PDT)
1. AquistToAmber.xls (21504 bytes)
[AMBER] Tleap problem with save prmtop and inpcrd file. can someone give me advice? hai wei (Sun Jul 17 2011 - 00:27:21 PDT)
1. leap.log (257187 bytes)
Re: [AMBER] Error in unit 9 inpcrd file KIRTANA S (Sun Jul 17 2011 - 19:36:23 PDT)
1. pmma_500mer.inpcrd (273834 bytes)
[AMBER] Periodicity in MD simulations Oliver Kuhn (Mon Jul 18 2011 - 11:17:35 PDT)
1. all.NW.c.angle.pdf (37187 bytes)
Re: [AMBER] PB calculation error when using MMPBSA.py Bill Miller III (Tue Jul 19 2011 - 03:28:33 PDT)
1. focusing.patch (12580 bytes)
Re: [AMBER] Periodicity in MD simulations Oliver Kuhn (Tue Jul 19 2011 - 22:30:43 PDT)
1. all.NW.c.bond.pdf (53508 bytes)
[AMBER] Fwd: Periodicity in MD simulations Oliver Kuhn (Tue Jul 19 2011 - 23:00:06 PDT)
1. all.NW.c.bond.pdf (53508 bytes)
[AMBER] Amber test failure haris p (Tue Jul 19 2011 - 23:41:33 PDT)
1. testlogp2 (76602 bytes)
2. testlog (56277 bytes)
[AMBER] Fwd: Periodicity in MD simulations Oliver Kuhn (Wed Jul 20 2011 - 00:43:39 PDT)
1. all.NW.c.bond.pdf (53508 bytes)
[AMBER] Fwd: Periodicity in MD simulations Oliver Kuhn (Wed Jul 20 2011 - 00:51:22 PDT)
1. all.NW.c.bond.pdf (53508 bytes)
[AMBER] Urea box: artifacts or just a special distribution? Na Le Dang (Wed Jul 20 2011 - 08:57:58 PDT)
1. Picture_2.png (424970 bytes)
[AMBER] H-bond vs. time Beale, John (Fri Jul 22 2011 - 03:06:46 PDT)
1. image001.jpg (23871 bytes)
[AMBER] reproducing a simulation Xiao Chen (Fri Jul 22 2011 - 04:34:35 PDT)
1. 20frames.xlsx (11145 bytes)
Re: [AMBER] problem with addIons in tleap Wei Chen (Fri Jul 22 2011 - 11:33:51 PDT)
1. 3ije.tif (645968 bytes)
[AMBER] configure_error Carmen Di Giovanni (Tue Jul 19 2011 - 10:44:37 PDT)
1. error_snapshot.docx (796926 bytes)
Re: [AMBER] Error in unit 9 inpcrd file KIRTANA S (Mon Jul 18 2011 - 11:44:46 PDT)
1. _Copy.mol2 (1025745 bytes)
[AMBER] AMBER10 pimd failure on =>16 cores Andrew Petersen (Wed Jul 27 2011 - 14:22:02 PDT)
1. test2.file (2603 bytes)
2. spcfw.rst.1 (47465 bytes)
3. spcfw.top (112127 bytes)
4. cmd.in (313 bytes)
[AMBER] MMPBSA yielding different values when processed with .prepin and .lib file sunita gupta (Thu Jul 28 2011 - 01:14:41 PDT)
1. Lib_file.txt (9689 bytes)
2. LI59bDRG.prepin (6159 bytes)
3. LI59b.mol2 (7239 bytes)
Re: [AMBER] possible problem with periodic cell Bruno Rodrigues (Thu Jul 28 2011 - 14:55:02 PDT)
1. system.png (436236 bytes)

Last message date: Sun Jul 31 2011 - 05:00:05 PDT
Archived on: Wed Nov 20 2024 - 05:54:12 PST

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