Amber Archive Mar 2011 by messages with attachments

Re: [AMBER] Restart Problem: The results of an integrated simulation and restarted simulations are not equal! Ali M. Naserian-Nik (Tue Mar 01 2011 - 00:42:52 PST)
1. 40ps_cgcaaaaaagcg_GB.pdb (41890 bytes)
2. 20_20ps_cgcaaaaaagcg_GB.pdb (41890 bytes)
[AMBER] hydrogen bonding facility in ptraj Beale, John (Fri Mar 04 2011 - 05:38:11 PST)
1. image001.jpg (2950 bytes)
2. hydbond.in (836 bytes)
[AMBER] missing AMBER features for simulating surfaces and linear assemblies Andrew Jewett (Mon Mar 07 2011 - 02:18:31 PST)
1. bubble.jpg (48600 bytes)
[AMBER] Pressure regulation and position restraints Andrew Jewett (Mon Mar 07 2011 - 04:33:36 PST)
1. virial_fixed_atoms.pdf (430406 bytes)
[AMBER] Fwd: Implicit solvent GB calculation Rubben Torella (Mon Mar 07 2011 - 07:04:35 PST)
1. md.in (650 bytes)
Re: [AMBER] Problems with tleap Pegado Luis (Tue Mar 08 2011 - 02:04:34 PST)
1. winmail.dat (3548 bytes)
Re: [AMBER] a question about using oplsaa ff in amber Ben Roberts (Tue Mar 08 2011 - 08:44:05 PST)
1. smime.p7s (2670 bytes)
Re: [AMBER] xleap not installed Ben Roberts (Tue Mar 08 2011 - 09:13:47 PST)
1. smime.p7s (2670 bytes)
Re: [AMBER] Problem installing Amber11/Ambertools1.4 on Ubuntu10.10 Ben Roberts (Tue Mar 08 2011 - 10:09:15 PST)
1. smime.p7s (2670 bytes)
[AMBER] about Nmod in amber11 juan zeng (Tue Mar 08 2011 - 23:25:11 PST)
1. sanmin_com.1.out (144419 bytes)
2. nmode_com.1.out (2064 bytes)
Re: [AMBER] Umbrella sampling coordinate question Rajesh Raju (Wed Mar 09 2011 - 10:55:38 PST)
1. cyclodextrin.jpg (52043 bytes)
Re: [AMBER] peek_ewald_inpcrd: SHOULD NOT BE HERE hari krishna (Wed Mar 09 2011 - 20:20:11 PST)
1. complex_sol.inpcrd (570029 bytes)
Re: [AMBER] Pressure regulation and position restraints Andrew Jewett (Thu Mar 10 2011 - 18:51:55 PST)
1. volume_vs_time_new.png (7530 bytes)
[AMBER] Query regarding mmpbsa output file Hirdesh Kumar (Fri Mar 11 2011 - 06:24:33 PST)
1. binding_energy.log (6161 bytes)
[AMBER] Amber Training Workshop Announcement - Barcelona, Spain. 3-6 May 2011 Ross Walker (Fri Mar 11 2011 - 10:24:53 PST)
1. brochure.pdf (422222 bytes)
[AMBER] AmberTools 1.4 possible bug for secstruct (test case attached) Tru Huynh (Fri Mar 11 2011 - 16:30:57 PST)
1. GSCASVCGV.pdb (8766 bytes)
2. GSCASVCGV.in (33 bytes)
3. GSCASVCGV.stride (1921 bytes)
4. GSCASVCGV.dssp (4339 bytes)
[AMBER] rdf plot subrata paul (Fri Mar 11 2011 - 19:54:29 PST)
1. OwOw_rdf_carnal.ps (20812 bytes)
Re: [AMBER] Query regarding mmpbsa output file Hirdesh Kumar (Fri Mar 11 2011 - 21:58:04 PST)
1. bindingE.log (6161 bytes)
2. pbsa_com.in (556 bytes)
3. pbsa_lig.in (556 bytes)
4. pbsa_rec.in (556 bytes)
5. sander_com.in (365 bytes)
6. sander_lig.in (365 bytes)
7. sander_rec.in (365 bytes)
8. snapshot_com.all.out (3503 bytes)
9. snapshot_lig.all.out (3390 bytes)
10. snapshot_rec.all.out (3503 bytes)
Re: [AMBER] Energy Decomposition using mmpbsa script Eliac Brown (Sat Mar 12 2011 - 07:32:36 PST)
1. binding_energy.mmpbsa (10192 bytes)
2. snapshot_statistics.out (1535 bytes)
3. mmpbsa.in (114 bytes)
4. FINAL_RESULTS_MMPBSA.dat (4069 bytes)
Re: [AMBER] error in creating prmtop and inpcrd files Ben Roberts (Sun Mar 13 2011 - 11:42:29 PDT)
1. smime.p7s (3919 bytes)
Re: [AMBER] error in creating prmtop and inpcrd files Chris Bryant (Sun Mar 13 2011 - 13:55:51 PDT)
1. Serpin1.pdb (476261 bytes)
Re: [AMBER] error in creating prmtop and inpcrd files Ben Roberts (Sun Mar 13 2011 - 14:34:48 PDT)
1. smime.p7s (3919 bytes)
Re: [AMBER] Would liek to plot GBTOT vs Time Jason Swails (Mon Mar 14 2011 - 00:02:28 PDT)
1. energyvectors.sh (5692 bytes)
[AMBER] Query regarding mmpbsa run Hirdesh Kumar (Mon Mar 14 2011 - 03:59:38 PDT)
1. bE.log (13016 bytes)
2. snapshot_com.all.out (3153 bytes)
3. snapshot_lig.all.out (3153 bytes)
4. snapshot_rec.all.out (3153 bytes)
[AMBER] Missing Parameters Melanie (Tue Mar 15 2011 - 10:29:32 PDT)
1. leap.log (16112 bytes)
[AMBER] Segmentation fault MASLYK, MACIEJ MARCIN (Wed Mar 16 2011 - 08:50:36 PDT)
1. Phe_nowat1.mol2 (874154 bytes)
Re: [AMBER] Missing Parameters Melanie (Thu Mar 17 2011 - 12:27:35 PDT)
1. 3NJW.pdb (45684 bytes)
2. 3NJW_old.pdb (45684 bytes)
Re: [AMBER] error installing AmberTools-1.2 in ubuntu 10.10 Ben Roberts (Thu Mar 17 2011 - 12:52:26 PDT)
1. smime.p7s (2670 bytes)
Re: [AMBER] Missing Parameters Ilyas Yildirim (Thu Mar 17 2011 - 12:59:00 PDT)
1. tmp.pdb (13797 bytes)
[AMBER] trouble with mmpbsa.py Chris Chris (Fri Mar 18 2011 - 09:44:08 PDT)
1. complex_schematic.pdf (24927 bytes)
2. mmpbsa_g1tetra.out (1245 bytes)
3. mmpbsa_g1tetra.err (873 bytes)
4. mmpbsa_g1tetra.in (117 bytes)
[AMBER] protein charge Ouaray Z. (Mon Mar 21 2011 - 06:52:23 PDT)
1. 2AHI_capmin.pdb (218316 bytes)
[AMBER] Nmode error of MMPBSA.py 陳昭同 (Wed Mar 23 2011 - 02:30:36 PDT)
1. 0.03.rar (670131 bytes)
[AMBER] tleap strange behavior Ignacio J. General (Wed Mar 23 2011 - 08:45:29 PDT)
1. testA.in (215 bytes)
2. testB.in (224 bytes)
3. 001_v0_l00.pdb (163341 bytes)
4. SB3.frcmod (641 bytes)
5. smallPBC-noSB3-testA.prmtop (293586 bytes)
6. smallPBC-noSB3-testB.prmtop (293586 bytes)
7. SB3.doc (9532 bytes)
[AMBER] odd output from rms measurement Chris Chris (Wed Mar 23 2011 - 14:55:44 PDT)
1. Decamer_RMS.pdf (450499 bytes)
[AMBER] Amber 姜笑楠 (Wed Mar 23 2011 - 23:50:08 PDT)
1. Catch2.jpg (51057 bytes)
2. 24-12-04-36_.jpg (133104 bytes)
Re: [AMBER] odd output from rms measurement 姜笑楠 (Thu Mar 24 2011 - 00:31:34 PDT)
1. Catch1.jpg (49608 bytes)
2. Catch0.jpg (255410 bytes)
Re: [AMBER] Ptraj crashes and Hbond analysis Kamali Sripathi (Thu Mar 24 2011 - 06:36:28 PDT)
1. dihedrals.out (1128 bytes)
2. dihedrals.ptraj (659 bytes)
3. distances.out (16659 bytes)
4. distances.ptraj (786 bytes)
Re: [AMBER] Sander was terminating in the midddle Ben Roberts (Thu Mar 24 2011 - 10:54:56 PDT)
1. smime.p7s (2670 bytes)
[AMBER] Amber Installation error Hirdesh Kumar (Fri Mar 25 2011 - 05:22:25 PDT)
1. amber-error (15249 bytes)
Re: [AMBER] Extract binding free energy for each snapshot Jason Swails (Fri Mar 25 2011 - 07:54:57 PDT)
1. energyvectors.sh (5692 bytes)
[AMBER] enzyme MD trajectory looks funny Mahmoud Soliman (Mon Mar 28 2011 - 06:10:38 PDT)
1. Picture_1.png (343266 bytes)
2. Picture_2.png (365400 bytes)
Re: [AMBER] RESP: optimized charges not reasonable Ignacio Faustino Plo (Tue Mar 29 2011 - 03:46:12 PDT)
1. resp.out (7602 bytes)
[AMBER] Loading .mol2 file in sleap r smith (Wed Mar 30 2011 - 06:12:15 PDT)
1. em_ac.mol2 (3029 bytes)
Re: [AMBER] Loading .mol2 file in sleap Ben Roberts (Wed Mar 30 2011 - 07:43:00 PDT)
1. smime.p7s (2670 bytes)
Re: [AMBER] Loading .mol2 file in sleap Ben Roberts (Wed Mar 30 2011 - 12:16:20 PDT)
1. smime.p7s (2670 bytes)
Re: [AMBER] Loading .mol2 file in sleap r smith (Wed Mar 30 2011 - 12:30:46 PDT)
1. em_ac.frcmod (626 bytes)
2. em_ac.mol2 (3024 bytes)
3. em_ac.pdb (2245 bytes)
Re: [AMBER] Loading .mol2 file in sleap Ben Roberts (Wed Mar 30 2011 - 13:19:21 PDT)
1. smime.p7s (2670 bytes)
[AMBER] segmentation fault when using mmpbsa.py Chris Chris (Wed Mar 30 2011 - 15:03:46 PDT)
1. mmpbsa_g1octa.out (1399 bytes)
2. mmpbsa_g1octa.err (5447 bytes)
Re: [AMBER] Loading .mol2 file in sleap Ben Roberts (Wed Mar 30 2011 - 20:16:59 PDT)
1. smime.p7s (3919 bytes)

Last message date: Thu Mar 31 2011 - 17:00:02 PDT
Archived on: Fri Dec 20 2024 - 05:54:17 PST

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