Amber Archive Mar 2009: by messages with attachments

RE: [AMBER] Question about NAB module Wei Huang (Sun Mar 01 2009 - 06:57:50 PST)
1. at_8.nab (8892 bytes)
[AMBER] angle between ligand ring plane and axis Jia Xu (Wed Mar 04 2009 - 03:00:08 PST)
1. 1W92.jpg (98690 bytes)
[AMBER] Thermodynamic Intergration problem Xiaohui Jiang [Contractor] (Wed Mar 04 2009 - 07:36:14 PST)
1. VDW_mdout_mini_v1_L0.5 (2840 bytes)
2. VDW_mdout_mini_v0_L0.5 (2840 bytes)
[AMBER] divcon error during antechamber run, convergence problem drugdesign (Thu Mar 05 2009 - 05:53:59 PST)
1. 0308.pdb (5937 bytes)
2. divcon.in (3072 bytes)
Re: [AMBER] catenan simulation problems Cristina S.D. Sisu (Fri Mar 06 2009 - 07:35:46 PST)
1. cat1.pdb (14644 bytes)
2. cat1.mol2 (18473 bytes)
3. cat_wat.pdb (344743 bytes)
4. cat1.frcmod (845 bytes)
Re: [AMBER] divcon error during antechamber run, convergence problem Andrew Voronkov (Fri Mar 06 2009 - 10:04:55 PST)
1. 0308.pdb (4205 bytes)
2. sustiva.pdb (1710 bytes)
[AMBER] addles segmentation fault gmail (Mon Mar 09 2009 - 01:28:56 PDT)
1. addles.out (525615 bytes)
2. addles.in (283 bytes)
Re: [AMBER] Seeking for suggestion related to plot the cluster out file S.Sundar Raman (Wed Mar 11 2009 - 07:57:40 PDT)
1. 1FBL_cluster.txt (305236 bytes)
Re: [AMBER] Problem running test.pmemd.AMOEBA Robert Duke (Fri Mar 13 2009 - 07:33:55 PDT)
1. amoeba_formbox.mdout (15978 bytes)
2. amoeba_jac.mdout (16138 bytes)
3. amoeba_wat1.out (16180 bytes)
4. amoeba_wat2.out (16233 bytes)
5. mdout.amoeba_gb1 (16150 bytes)
6. ATT29216851.txt (137 bytes)
[AMBER] Unit 5 Error on OPEN: nan.in Nancy (Mon Mar 16 2009 - 05:49:31 PDT)
1. nan.in (186 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Mon Mar 16 2009 - 06:29:37 PDT)
1. lex.dg_options.c (20711 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] about mm-pbsa 廖青华 (Mon Mar 16 2009 - 08:02:49 PDT)
1. mm_pbsa.log (1465 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] mol2 - pdb conversion Taufik Al-Sarraj (Mon Mar 16 2009 - 14:38:09 PDT)
1. SiO2APTMS.mol2 (405601 bytes)
2. mysioforce.frcmod (3584 bytes)
3. ATT00002.txt (137 bytes)
[AMBER] Unit 5 Error on OPEN: nan.in Nancy (Tue Mar 17 2009 - 02:11:10 PDT)
1. nan.in (186 bytes)
2. nan.out (276 bytes)
3. ATT00002.txt (137 bytes)
[AMBER] CCL4 simulation sudipta (Tue Mar 17 2009 - 11:18:07 PDT)
1. NEWPDB_c.prmtop (8615 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] protein protrudes from unit cell Jeffrey (Wed Mar 18 2009 - 01:59:06 PDT)
1. ATT00002.txt (137 bytes)
[AMBER] About mm-pbsa 廖青华 (Wed Mar 18 2009 - 23:48:21 PDT)
1. binding.rar (57172 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] problem in running sander Kshatresh Dutta Dubey (Thu Mar 19 2009 - 00:17:21 PDT)
1. test_result (25966 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] error for nmode Dechang Li (Thu Mar 19 2009 - 04:00:09 PDT)
1. ATT00002.txt (137 bytes)
Re: [AMBER] temperature rises with igb=1 Bala subramanian (Thu Mar 19 2009 - 04:24:45 PDT)
1. a.pdf (61578 bytes)
2. b.pdf (58892 bytes)
3. ATT00002.txt (137 bytes)
Re: [AMBER] pmemd compile error.... Robert Duke (Thu Mar 19 2009 - 08:25:04 PDT)
1. pmemd_memory_requirements.wmf (20698 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] Parametrisation of Silicon based molecules for Amber simulations ? Marek Malý (Thu Mar 19 2009 - 16:49:21 PDT)
1. mol.prmtop (20785 bytes)
2. mol.pdb (3053 bytes)
3. mol01.jpg (16991 bytes)
4. mol02.jpg (17083 bytes)
5. mol.frcmod (1168 bytes)
6. mol.inpcrd (1286 bytes)
7. mol.prepin (2902 bytes)
8. ATT00002.txt (137 bytes)
Re: [AMBER] please help me out bharat lakhani (Mon Mar 23 2009 - 00:58:52 PDT)
1. DDD7.pdb (532070 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] leap and chirality Karl Kirschner (Mon Mar 23 2009 - 02:54:29 PDT)
1. leap.in (172 bytes)
2. res_a.prep (1084 bytes)
3. res_b.prep (1089 bytes)
4. ATT00002.txt (137 bytes)
Re: [AMBER] leap and chirality Wei Zhang (Mon Mar 23 2009 - 11:36:54 PDT)
1. chir.patch (22390 bytes)
2. ATT00003.txt (1516 bytes)
3. ATT00004.txt (137 bytes)
[AMBER] errors on reading time series file in WHAM calculation gmail (Mon Mar 23 2009 - 17:35:02 PDT)
1. ATT00002.txt (137 bytes)
Re: [AMBER] leap and chirality Karl Kirschner (Tue Mar 24 2009 - 01:11:38 PDT)
1. res_a.prep (1084 bytes)
2. res_b.prep (1089 bytes)
3. ATT00002.txt (137 bytes)
[AMBER] Problem reading PDB file into XLEAP Hopkins, Robert (Thu Mar 26 2009 - 17:01:26 PDT)
1. DDIRinmin.pdb (41780 bytes)
2. IRin_sol.pdb (914245 bytes)
3. leap.log (298110 bytes)
4. ATT00002.txt (137 bytes)
[AMBER] Antechamber problem 欧阳德方 (Thu Mar 26 2009 - 21:44:24 PDT)
1. 4_arginine.pdb (7001 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] problem in installing AMBER10 Dr. Debaprasad Giri (Fri Mar 27 2009 - 03:16:47 PDT)
1. error (10041 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] Problem with "Atom does not have a type" Richard Tseng (Fri Mar 27 2009 - 15:08:34 PDT)
1. NTA.pdb (1494 bytes)
2. NTC.pdb (1358 bytes)
3. NTG.pdb (1562 bytes)
4. NTU.pdb (1596 bytes)
5. ATT00002.txt (137 bytes)
RE: [AMBER] Problem reading PDB file into XLEAP Hopkins, Robert (Fri Mar 27 2009 - 15:09:11 PDT)
1. DDsolmin.in (291 bytes)
2. ATT00002.txt (137 bytes)
RE: [AMBER] Problem reading PDB file into XLEAP - SLEAP Hopkins, Robert (Sat Mar 28 2009 - 16:12:06 PDT)
1. ATT00002.txt (137 bytes)
[AMBER] .rst file generation problem. Aravind S (Sun Mar 29 2009 - 22:48:55 PDT)
1. dna_wat_mdfiinal.in (287 bytes)
2. dna_wat_mdfiinal.out (6285 bytes)
3. dna_wat_4min5.rst (538253 bytes)
4. ATT00002.txt (137 bytes)
[AMBER] "rfree: End of file on unit 5" Remya S R (Sun Mar 29 2009 - 23:21:53 PDT)
1. dna_fmd.in (309 bytes)
2. dnafmd.out (6433 bytes)
3. dna_min55.in (202 bytes)
4. ATT00002.txt (137 bytes)
[AMBER] amber tools installation Jayalakshmi Sridhar (Mon Mar 30 2009 - 08:44:57 PDT)
1. jsridhar.vcf (203 bytes)
2. ATT00002.txt (137 bytes)

Amber Archive Mar 2009 by messages with attachments