Amber Archive Apr 2017 by messages with attachments

[AMBER] Acetonitrile Water Mix Andreas Tosstorff (Wed Apr 05 2017 - 05:35:31 PDT)
1. 04-05_14-05-36.png (139611 bytes)
2. 04-05_14-06-30.png (162358 bytes)
3. 04-05_14-06-54.png (263783 bytes)
4. prd.in (196 bytes)
5. min.in (61 bytes)
6. eq_v.in (218 bytes)
7. eq_pt.in (233 bytes)
Re: [AMBER] Atom types for Baaden Hydronium Ion Samaneh Ghassabi Kondalaji (Wed Apr 05 2017 - 09:06:39 PDT)
1. PREPH3O.DAT (425 bytes)
2. H3O_.pdb (401 bytes)
3. H3O_.in (133 bytes)
4. frcmod.H3O (253 bytes)
Re: [AMBER] Acetonitrile Water Mix Andreas Tosstorff (Wed Apr 05 2017 - 09:08:53 PDT)
1. 20721_ftp.pdf (381468 bytes)
[AMBER] Diffusion and permeability coefficients Fabrício Bracht (Thu Apr 06 2017 - 12:01:19 PDT)
1. diffusion1.png (8544 bytes)
2. free.png (40130 bytes)
Re: [AMBER] Acetonitrile Water Mix Marcos Serrou do Amaral (Fri Apr 07 2017 - 05:58:51 PDT)
1. model.mol2 (805 bytes)
2. ACN_model.prm (561 bytes)
Re: [AMBER] Minimization fails when switching from steepest descent to conjugate gradient Andreas Tosstorff (Sun Apr 09 2017 - 14:40:02 PDT)
1. 04-09_23-26-37.png (267813 bytes)
[AMBER] QM/MM equilibration before SMD in vacuum Samaneh Ghassabi Kondalaji (Mon Apr 10 2017 - 09:04:21 PDT)
1. K12_WAT_qmmm_equil.out (30411 bytes)
2. K12_WAT.prmtop (124556 bytes)
3. min.rst (7084 bytes)
4. Dist_RST.dat (133 bytes)
5. Equil_QMMM.in (635 bytes)
[AMBER] DNA Tutorial B1 - Temperature Drop Johannes Kalliauer (Tue Apr 11 2017 - 02:42:42 PDT)
1. summary.png (5199 bytes)
Re: [AMBER] cpptraj creates pdb file it cannot read James Kress (Tue Apr 11 2017 - 13:44:09 PDT)
1. frame_1.zip (260937 bytes)
2. frame_1000.zip (262111 bytes)
Re: [AMBER] cpptraj creates pdb file it cannot read James Kress (Tue Apr 11 2017 - 14:03:17 PDT)
1. md3_new.zip (260763 bytes)
[AMBER] Discrepancy in delta G total and per residues decomposition results in MMPBSA.py mish (Wed Apr 12 2017 - 01:35:32 PDT)
1. PBSA-GB1.dat (109244 bytes)
2. PBSA-GB1.dat (6354 bytes)
[AMBER] antechamber problem Maura Malinska (Wed Apr 12 2017 - 06:59:37 PDT)
1. CB6.pdb (11093 bytes)
2. sqm.out (24976 bytes)
[AMBER] Format error in frcmod file of HEME Thakur, Abhishek (Fri Apr 14 2017 - 09:42:46 PDT)
1. HEME.frcmod (3034 bytes)
Re: [AMBER] coordinate bond between them and S and FE Thakur, Abhishek (Mon Apr 17 2017 - 07:45:31 PDT)
1. 04-17_at_10.44.19_AM.png (234041 bytes)
Re: [AMBER] coordinate bond between them and S and FE Thakur, Abhishek (Mon Apr 17 2017 - 08:38:55 PDT)
1. 04-17_at_11.37.56_AM.png (106618 bytes)
Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Samaneh Ghassabi Kondalaji (Mon Apr 17 2017 - 11:36:58 PDT)
1. K12_WAT_Equil_1.rst (13736 bytes)
2. K12_WAT.prmtop (124556 bytes)
Re: [AMBER] HEME-CYS Elvis Martis (Tue Apr 18 2017 - 08:22:26 PDT)
1. heme.frcmod (3759 bytes)
2. HEM_CPD.mol2 (7460 bytes)
3. HEM.inpcrd (2681 bytes)
4. HEM.prmtop (39765 bytes)
[AMBER] 3D-RISM centering 0 Lucia Fusani (Thu Apr 20 2017 - 10:05:42 PDT)
1. image001.png (11130 bytes)
2. centering0.jpeg (55186 bytes)
Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? Guqin Shi (Fri Apr 21 2017 - 07:58:01 PDT)
1. 1.png (102834 bytes)
[AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 Mooers, Blaine H.M. (HSC) (Fri Apr 21 2017 - 12:36:27 PDT)
1. 04-19_10-36-17.log (142532 bytes)
[AMBER] failed to generate parameter and topology file for protein-ligand complex containing zinc Sharon D. Morris (Sat Apr 22 2017 - 02:00:17 PDT)
1. 3.png (74888 bytes)
2. 2.png (75317 bytes)
Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 Mooers, Blaine H.M. (HSC) (Sat Apr 22 2017 - 14:01:02 PDT)
1. 04-22_15-03-50.log (35005 bytes)
Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Adams, John E. (Fri Apr 28 2017 - 14:59:15 PDT)
1. LG1.mol2 (8691 bytes)
2. LIG.frcmod (2788 bytes)
3. ZR1.mol2 (263 bytes)
4. ZRLIG_mcpbpy.frcmod (12372 bytes)
5. ZRLIG_mcpbpy.pdb (5996 bytes)
6. ZRLIG_tleap.in (923 bytes)
7. Test_failures.log (14858 bytes)
Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Adams, John E. (Fri Apr 28 2017 - 15:24:10 PDT)
1. config.h (6319 bytes)

Last message date: Sun Apr 30 2017 - 17:30:03 PDT
Archived on: Sun Nov 24 2024 - 05:55:42 PST

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