Amber Archive May 2011 by messages with attachments

Re: [AMBER] MCPB help Hashem Taha (Tue May 03 2011 - 08:51:19 PDT)
1. 1HZY_OH_large_mk.resp1 (3740 bytes)
2. 1HZY_OH_large_mk.resp2 (3766 bytes)
[AMBER] MCPB problem Manish (Tue May 03 2011 - 09:31:36 PDT)
1. prot1.pdb_large.log.gz (114185 bytes)
Re: [AMBER] MCPB help Ben Roberts (Tue May 03 2011 - 14:21:07 PDT)
1. smime.p7s (2670 bytes)
Re: [AMBER] MCPB problem Ben Roberts (Tue May 03 2011 - 14:20:18 PDT)
1. smime.p7s (2670 bytes)
Re: [AMBER] MCPB problem Manish (Wed May 04 2011 - 08:22:00 PDT)
1. prot1.pdb_large_60hrs.bcl (4954 bytes)
2. prot1.pdb_large.bcl (5164 bytes)
3. prot1.pdb_large.log.gz (115370 bytes)
Re: [AMBER] Loading .mol2 file in sleap Ben Roberts (Wed May 04 2011 - 11:26:37 PDT)
1. smime.p7s (2670 bytes)
Re: [AMBER] MTK++ MCPB Example: Creating Force Field Modification Files Ben Roberts (Wed May 04 2011 - 11:29:49 PDT)
1. smime.p7s (2670 bytes)
[AMBER] Xleap trouble souvik sur (Wed May 04 2011 - 23:53:11 PDT)
1. Xleap.zip (191225 bytes)
2. DMA_protonated.pdb (9534 bytes)
3. 33342.pdb (9389 bytes)
Re: [AMBER] MTK++/MCPB Error Loading AMBER prep file 1AMP_OH_chg2.prep in xleap Naveen Samala (Thu May 05 2011 - 07:52:55 PDT)
1. 1AMP_OH_chg2.prep (8442 bytes)
Re: [AMBER] MTK++/MCPB Error Loading AMBER prep file 1AMP_OH_chg2.prep in xleap Naveen Samala (Thu May 05 2011 - 08:53:56 PDT)
1. 1AMP_OH_chg2.xml1 (71943 bytes)
[AMBER] MMPBSA: Trajectory pre-processing George Tzotzos (Fri May 06 2011 - 03:30:05 PDT)
1. image.png (347225 bytes)
Re: [AMBER] forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read Katharina Lang (Fri May 06 2011 - 07:54:07 PDT)
1. smime.p7s (5473 bytes)
[AMBER] Problem in preparation of log file Sindrila Dutta banik (Sat May 07 2011 - 00:50:08 PDT)
1. DNA.pdb (62900 bytes)
2. leap.log (139967 bytes)
[AMBER] NMODE calculations results doubtful vaibhav dixit (Sun May 08 2011 - 21:46:43 PDT)
1. FINAL_RESULTS_MMPBSA.dat (9206 bytes)
Re: [AMBER] NMODE calculations results doubtful vaibhav dixit (Sun May 08 2011 - 23:34:49 PDT)
1. _MMPBSA_complex_nm.out (10920 bytes)
2. _MMPBSA_ligand_nm.out (19835 bytes)
[AMBER] nmode calculation Sangita Kachhap (Mon May 09 2011 - 10:42:16 PDT)
1. A_FINAL_RESULTS_MMPBSA.dat (2281 bytes)
2. A_FINAL_RESULTS_MMPBSA.dat (2281 bytes)
3. A_FINAL_RESULTS_MMPBSA.dat (2281 bytes)
Re: [AMBER] Questions about compiling AmberToolsv1.4 Kamali Sripathi (Mon May 09 2011 - 11:07:20 PDT)
1. 05-09_10-31-36.log (62809 bytes)
Re: [AMBER] new lib loaded, but atom types are not recognized Chinh Su Tran To (Tue May 10 2011 - 01:05:53 PDT)
1. hiz_lib.txt (3336 bytes)
Re: [AMBER] Questions about compiling AmberToolsv1.4 Kamali Sripathi (Tue May 10 2011 - 05:09:58 PDT)
1. config.h (3683 bytes)
[AMBER] system imaging Alex Rodriguez (Tue May 10 2011 - 09:09:36 PDT)
1. tic_md_rmsd_new.dat (1000 bytes)
Re: [AMBER] how to use Bennett acceptance ratio in Amber11? steinbrt.rci.rutgers.edu (Thu May 12 2011 - 00:52:22 PDT)
1. prepare_mbar_data.pl (2369 bytes)
[AMBER] Problem with Equilibration Devlina Chakravarty (Thu May 12 2011 - 05:13:58 PDT)
1. 1sa0.equil.out (5821 bytes)
[AMBER] strange volume contraction Massimiliano Porrini (Fri May 13 2011 - 05:51:34 PDT)
1. graph.eps (56032 bytes)
Re: [AMBER] error in protein miniminisation Ben Roberts (Fri May 13 2011 - 06:06:48 PDT)
1. smime.p7s (2670 bytes)
[AMBER] segmentation fault when running sander Chinh Su Tran To (Sun May 15 2011 - 21:42:40 PDT)
1. md1.in (334 bytes)
[AMBER] error preparing a ligand using antechamber Paul Rigor (Mon May 16 2011 - 14:18:17 PDT)
1. lycopene_h.pdb (3291 bytes)
Re: [AMBER] error preparing a ligand using antechamber Paul Rigor (Mon May 16 2011 - 17:31:11 PDT)
1. lycopenepdb_h.pdb (4317 bytes)
[AMBER] rst problem Sel Ercan (Tue May 17 2011 - 00:31:23 PDT)
1. md.in (344 bytes)
2. 1.out (3039 bytes)
3. md1rst.rar (370415 bytes)
[AMBER] rst problem selami ercan (Tue May 17 2011 - 01:23:47 PDT)
1. md.in2 (328 bytes)
2. 1.out (3039 bytes)
3. md1rst.rar (370415 bytes)
[AMBER] rst problem Sel Ercan (Tue May 17 2011 - 01:44:52 PDT)
1. md.in (344 bytes)
2. 1.out (3039 bytes)
Re: [AMBER] regarding LINMIN failure Ben Roberts (Wed May 18 2011 - 08:06:19 PDT)
1. smime.p7s (2670 bytes)
[AMBER] antechamber ERROR George Tzotzos (Wed May 18 2011 - 11:24:35 PDT)
1. ligand.pdb (3043 bytes)
Re: [AMBER] segmentation fault when running sander Chinh Su Tran To (Wed May 18 2011 - 18:49:22 PDT)
1. inputs.rar (718617 bytes)
2. ndm_md1.out (8534 bytes)
Re: [AMBER] segmentation fault when running sander Chinh Su Tran To (Wed May 18 2011 - 21:48:39 PDT)
1. leap_log.txt (43343 bytes)
2. Zn.frcmod (936 bytes)
[AMBER] Solvation Sindrila Dutta banik (Thu May 19 2011 - 04:11:05 PDT)
1. Pro_Str_Func_Gene_1998_32_362.pdf (928833 bytes)
[AMBER] Ptraj NAMD dcd imaging Manish (Thu May 19 2011 - 10:01:34 PDT)
1. water_imaging.png (46537 bytes)
[AMBER] compilation of amber tools 1.5 with intel 11.1.059 Vlad Cojocaru (Fri May 20 2011 - 06:35:49 PDT)
1. make_at_serial.log (384456 bytes)
Re: [AMBER] compilation of amber tools 1.5 with intel 11.1.059 Daniel Roe (Fri May 20 2011 - 12:32:58 PDT)
1. Frame.cpp (28981 bytes)
[AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Paul Rigor (Wed May 25 2011 - 00:49:18 PDT)
1. 05-25_00-32-38.log (11589 bytes)
2. 05-25_00-32-38.diff (51705 bytes)
[AMBER] PROBLEM IN TERMINAL RESIDUES: WRONG BONDS Sindrila Dutta banik (Wed May 25 2011 - 09:10:00 PDT)
1. 1ASZ.pdb (998973 bytes)
Re: [AMBER] MCPB help Hashem Taha (Wed May 25 2011 - 09:19:08 PDT)
1. 1HZY_ZN_addStdMol.bcl (2674 bytes)
2. 1HZY_ZN_fixed.pdb (176714 bytes)
3. 1HZY_ZN_large_mk.log (613554 bytes)
4. 1HZY_ZN_large.bcl (4823 bytes)
5. 1HZY_ZN_sidechain.bcl (3812 bytes)
6. genMetalFF.sh (17779 bytes)
7. run.MCPB.csh (4260 bytes)
Re: [AMBER] CHAMBER Seibold, Stephen (Wed May 25 2011 - 11:18:00 PDT)
1. 6hyperchloro_gnoh.pdb.gz (84831 bytes)
2. 6hyperchloro_gnoh.psf.gz (147886 bytes)
3. par_all22_prot.prm.gz (23577 bytes)
4. 2Chamber.in.gz (158 bytes)
Re: [AMBER] AmberTools 1.5 and Amber11 Ben Roberts (Wed May 25 2011 - 11:41:19 PDT)
1. smime.p7s (2670 bytes)
Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Paul Rigor (Wed May 25 2011 - 17:53:37 PDT)
1. list.tar.bz2 (34523 bytes)
[AMBER] ibelly error qiaoyan (Wed May 25 2011 - 18:40:30 PDT)
1. md1.png (332199 bytes)
2. md2.png (144089 bytes)
3. md1.in (422 bytes)
4. md2.in (422 bytes)
Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Paul Rigor (Wed May 25 2011 - 18:51:43 PDT)
1. 05-25_18-22-30.diff (51705 bytes)
2. 05-25_18-22-30.log (11589 bytes)
Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Paul Rigor (Wed May 25 2011 - 19:19:21 PDT)
1. 05-25_19-11-35.log (11062 bytes)
Re: [AMBER] MCPB help Hashem Taha (Thu May 26 2011 - 12:14:52 PDT)
1. 1HZY_ZN_addStdMol.bcl (2674 bytes)
2. 1HZY_ZN_fixed.pdb (176714 bytes)
3. 1HZY_ZN_large.bcl (4823 bytes)
4. 1HZY_ZN_sidechain.bcl (3812 bytes)
5. genMetalFF.sh (17779 bytes)
6. run.MCPB.csh (4260 bytes)
Re: [AMBER] MCPB help Hashem Taha (Thu May 26 2011 - 12:15:18 PDT)
1. 1HZY_ZN_large_mk.log (613554 bytes)
Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Paul Rigor (Thu May 26 2011 - 23:34:27 PDT)
1. 05-26_22-07-35.log (7030 bytes)
2. 05-26_22-07-35.diff (614 bytes)
[AMBER] AMBER11 Installation on FEDORA 15 Vivek Shankar Bharadwaj (Fri May 27 2011 - 10:00:21 PDT)
1. configure_output_AmberTools.odt (11934 bytes)
2. make_output_AmberTools.odt (14902 bytes)
Re: [AMBER] MMPBSA nmode warning Sangita Kachhap (Sat May 28 2011 - 09:45:37 PDT)
1. FINAL_RESULTS_MMPBSA.dat (2370 bytes)
Re: [AMBER] AMBER11 Installation on FEDORA 15 case (Sun May 29 2011 - 10:54:46 PDT)
1. hofc.patch (813 bytes)
[AMBER] H-bond analysis Wu Xu (Mon May 30 2011 - 05:01:51 PDT)
1. analyse_hbond.out (19768 bytes)
Re: [AMBER] H-bond analysis Wu Xu (Mon May 30 2011 - 15:25:46 PDT)
1. analyse_hbond_1.out (123554 bytes)
Re: [AMBER] AMBER11 Installation on FEDORA 15 case (Mon May 30 2011 - 18:43:38 PDT)
1. hof.patch (1858 bytes)
Re: [AMBER] hold H-bonds of ssRNA fixed Wu Xu (Mon May 30 2011 - 19:17:12 PDT)
1. dmlliFold.pdb (274113 bytes)
2. dmllt1_wat_min1.in (200 bytes)
3. dmllt1_wat_min2.in (156 bytes)
4. dmllt1_wat_md1.in (324 bytes)
5. dmllt1_wat_md2.in (286 bytes)
Re: [AMBER] Normal Mode Analysis Deák Robi (Tue May 31 2011 - 00:48:56 PDT)
1. nmode.zip (66602 bytes)
[AMBER] Restraints during relaxation - add Oliver Kuhn (Tue May 31 2011 - 06:03:22 PDT)
1. all.NW.c.angle.pdf (37311 bytes)
2. all.NW.c.angle.pdf (37187 bytes)
[AMBER] Configuration Checking souvik sur (Tue May 31 2011 - 06:41:47 PDT)
1. Workstation_quote_hp.doc (36352 bytes)
[AMBER] MTK++/MCPB: Problem in converting prep to xml Naveen Samala (Tue May 31 2011 - 15:19:03 PDT)
1. sf4.prep (1005 bytes)

Last message date: Tue May 31 2011 - 21:00:02 PDT
Archived on: Mon Dec 23 2024 - 05:54:14 PST

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