Amber Archive Sep 2014 by messages with attachments

Re: [AMBER] meeting a problem when using ptraj to extract the replica exchanging self-guided MD trajectory wliu (Wed Sep 03 2014 - 02:58:57 PDT)
1. md.tar.bz2__size_486445 (486445 bytes)
[AMBER] QM/MM optimization error 王珍 (Sun Sep 07 2014 - 19:46:32 PDT)
1. 09-08_10:44:25.png (36518 bytes)
Re: [AMBER] Calculation of Urea_Urea Interaction energy MOHD HOMAIDUR RAHMAN (Mon Sep 08 2014 - 00:56:30 PDT)
1. ja0685506.pdf (94428 bytes)
Re: [AMBER] mismatch pdb files when created using ambpdb and savepdb sunita.tifrh.res.in (Wed Sep 10 2014 - 01:47:21 PDT)
1. minimized_structure.pdb (137216 bytes)
[AMBER] the out file of qm/mm in amber 王珍 (Wed Sep 10 2014 - 05:09:22 PDT)
1. ______1.png (15759 bytes)
2. old.gau_job.log (47353 bytes)
Re: [AMBER] Equilibration phase and RMSD Ibrahim Said (Thu Sep 11 2014 - 12:18:17 PDT)
1. equilib (22853 bytes)
[AMBER] CHAMBER: problem with water and swissparam generated ligand Eric Lang (Mon Sep 15 2014 - 13:59:53 PDT)
1. test.tar.gz (15783 bytes)
[AMBER] Simulating Silver Salt Soumendranath Bhakat (Wed Sep 17 2014 - 03:56:31 PDT)
1. silver_salt.docx (35835 bytes)
[AMBER] Clustering problem Alessandro Mariani (Wed Sep 17 2014 - 04:43:00 PDT)
1. example10x10.doc (47616 bytes)
2. program.rtf (1913 bytes)
Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand Eric Lang (Wed Sep 17 2014 - 07:48:04 PDT)
1. fragment.tar.gz (50817 bytes)
[AMBER] Error: cannot run Vishal Nemaysh (Thu Sep 18 2014 - 02:50:12 PDT)
1. 1YCC_h.pdb (138490 bytes)
Re: [AMBER] Two questions about Net charge and write frcmod in parmed.py Arun Srikanth (Thu Sep 18 2014 - 11:32:16 PDT)
1. epon.top (30098 bytes)
2. epon.frcmod (3392 bytes)
3. epon.mol2 (5445 bytes)
[AMBER] Hbond Difference For Ambertools 12 and 14, or bug leexa.intern.bii.a-star.edu.sg (Sun Sep 21 2014 - 23:37:41 PDT)
1. HB_1909.log__size_9372 (9373 bytes)
2. avgout_1909.out__size_14043 (14044 bytes)
[AMBER] Sudden change of energies in min.out files maryam azimzadehirani (Mon Sep 22 2014 - 03:15:40 PDT)
1. transition_path_2.pdf (35487 bytes)
Re: [AMBER] Hbond Difference For Ambertools 12 and 14, or bug leexa.intern.bii.a-star.edu.sg (Mon Sep 22 2014 - 17:56:55 PDT)
1. avgout_14_1909.out__size_14043 (14044 bytes)
2. HB_14_1909.log__size_9372 (9373 bytes)
3. HB_12_log_v4.log__size_33486 (33488 bytes)
[AMBER] How can I run Production MD for lipid in Amber12 using Lipid11-ff? Bikash Ranjan Sahoo (Tue Sep 23 2014 - 01:06:31 PDT)
1. 05_Prod.in (295 bytes)
[AMBER] Fwd: file contains 2 atoms not in residue templates Vishal Nemaysh (Tue Sep 23 2014 - 06:24:57 PDT)
1. 1YCC.pdb (67938 bytes)
[AMBER] why the same structure and same topology have different energies using CHARMM and AMBER ? wliu (Tue Sep 23 2014 - 07:52:11 PDT)
1. test.tar.gz__size_99554 (99554 bytes)
[AMBER] Parameter bond and angle file could not find Vishal Nemaysh (Wed Sep 24 2014 - 06:39:27 PDT)
1. 1YCC.pdb (67938 bytes)
2. 1YCC_final.pdb (112710 bytes)
[AMBER] FATAL: Atom .R.A does not have a type Soumendranath Bhakat (Fri Sep 26 2014 - 08:21:04 PDT)
1. rec_apo.pdb (205515 bytes)
[AMBER] Parameter file was not saved. Vishal Nemaysh (Mon Sep 29 2014 - 06:38:05 PDT)
1. dna.pdb (62245 bytes)

Last message date: Tue Sep 30 2014 - 16:00:02 PDT
Archived on: Wed Dec 25 2024 - 05:55:01 PST

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