Amber Archive Dec 2015 by thread
- [AMBER] mac hangs when compile ambertools15 on El capitan Yong Yao (Mon Nov 30 2015 - 19:13:31 PST)
- Re: [AMBER] Not matching test AMBER14 with CUDA Mijiddorj Batsaikhan (Mon Nov 30 2015 - 20:20:13 PST)
- [AMBER] How to run two single-card jobs on the node with two GPU cards Stephen Wang (Mon Nov 30 2015 - 22:25:57 PST)
- [AMBER] Utilizing two different nodes simultaneously for one job muhammad tahir ayub (Mon Nov 30 2015 - 22:35:26 PST)
- [AMBER] Docking before MD of scratch ligands OR not muhammad tahir ayub (Mon Nov 30 2015 - 23:49:57 PST)
- Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond V. Kumar (Mon Nov 30 2015 - 23:52:56 PST)
- Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) Nikolay N. Kuzmich (Tue Dec 01 2015 - 01:08:49 PST)
- [AMBER] mmgbsa_CalcError Atila Petrosian (Tue Dec 01 2015 - 04:13:48 PST)
- [AMBER] malloc error during MM-PBSA calculation on AMBER14 ... mmpbsa_py_energy: malloc.c:2372: sysmalloc Mijiddorj Batsaikhan (Tue Dec 01 2015 - 08:44:19 PST)
- [AMBER] [Amber] nmode() results with imaginary frequencies Guqin Shi (Tue Dec 01 2015 - 15:18:17 PST)
- [AMBER] How does the collision frequency gamma_ln value affect the temperature in Langevin dynamics jfliu (Tue Dec 01 2015 - 18:07:17 PST)
- [AMBER] Can I use the Nose-Hoover thermostat in Amber jfliu (Tue Dec 01 2015 - 18:12:54 PST)
- [AMBER] bug or not bug ???? Min Li (Tue Dec 01 2015 - 19:54:38 PST)
- [AMBER] Principal Component Analysis Beale, John (Wed Dec 02 2015 - 02:23:57 PST)
- [AMBER] kinetic Ziba Bahadori (Wed Dec 02 2015 - 04:14:32 PST)
- Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Wed Dec 02 2015 - 04:41:31 PST)
- [AMBER] pH-REMD GPU runs Arjun Sharma (Wed Dec 02 2015 - 05:53:22 PST)
- [AMBER] High PB deltaG values from MMPBSA.py calculation anu chandra (Wed Dec 02 2015 - 05:59:48 PST)
- [AMBER] Amber calculated structure(PDB) visualization in pymol vs chimera V. Kumar (Wed Dec 02 2015 - 11:38:00 PST)
- [AMBER] bond connections mohammad r (Wed Dec 02 2015 - 23:02:03 PST)
- [AMBER] AMBER 12 XLEAP options were disabled V. Kumar (Thu Dec 03 2015 - 03:36:58 PST)
- [AMBER] Simulation of the docked complex with phosphorylated tyrosine Pallavi Mohanty (Thu Dec 03 2015 - 03:53:38 PST)
- [AMBER] xleap terminal terminate Ayesha Kanwal (Thu Dec 03 2015 - 04:33:08 PST)
- [AMBER] pmemd.cuda with CoM restraints 達南杰 (Thu Dec 03 2015 - 06:56:20 PST)
- [AMBER] QM/MM Implementation Details Jim William Snyder Jr (Thu Dec 03 2015 - 10:38:35 PST)
- [AMBER] problem with "closest" waters being wrapped Kalenkiewicz, Andrew (NIH/NICHD) [F] (Thu Dec 03 2015 - 13:17:57 PST)
- [AMBER] Question Regarding Input File Preparation Ziheng Wang (Thu Dec 03 2015 - 18:35:49 PST)
- [AMBER] Add charges to new molecule with out Gaussian package V. Kumar (Sat Dec 05 2015 - 06:08:41 PST)
- [AMBER] per-residue or pairwise per-residue basis in decomposing the free energy contributions to the binding free energy Andrew Bostick (Sat Dec 05 2015 - 11:20:19 PST)
- [AMBER] standard deviation of Hbond lengths and angles Hadeer ELHabashy (Sun Dec 06 2015 - 07:20:12 PST)
- [AMBER] per-residue or pairwise per-residue basis in decomposing the free energy contributions to the binding free energy Andrew Bostick (Sun Dec 06 2015 - 10:45:18 PST)
- [AMBER] cpptraj: grid and gist Thomas Fox (Mon Dec 07 2015 - 02:22:19 PST)
- [AMBER] weird output of SMD simulation combined with Constant pH zhonghe xu (Mon Dec 07 2015 - 06:25:27 PST)
- [AMBER] External forces Jack Shepherd (Mon Dec 07 2015 - 09:29:07 PST)
- [AMBER] MMPBSA bad atom type error persisting Kenneth Huang (Mon Dec 07 2015 - 10:40:13 PST)
- Re: [AMBER] xparmed.py Nathalie Willems (Tue Dec 08 2015 - 07:23:19 PST)
- [AMBER] Amber 14, sander.MPI, NaN Starovoytov, Oleg (Tue Dec 08 2015 - 12:38:07 PST)
- [AMBER] problem with hist command in cpptraj in AmberTools15 Osman, Roman (Tue Dec 08 2015 - 12:59:46 PST)
- [AMBER] [Amber] Imaginary Frequencies from nmode() Guqin Shi (Tue Dec 08 2015 - 13:19:53 PST)
- [AMBER] Problem with GPU equilibration step [ cudaMalloc GpuBuffer::Allocate failed out of memory] Yogeeshwar Ajjugal (Tue Dec 08 2015 - 21:42:25 PST)
- Re: [AMBER] FW: FW: How to use "divergence" command Mahendra B Thapa (Wed Dec 09 2015 - 05:08:30 PST)
- [AMBER] Charmm-gui conversion mohammad r (Wed Dec 09 2015 - 08:02:20 PST)
- [AMBER] OSX 10.11.1: Amber installation problem George Tzotzos (Wed Dec 09 2015 - 10:19:47 PST)
- [AMBER] gnu plot of cpptraj Secstruct George Tzotzos (Thu Dec 10 2015 - 13:42:20 PST)
- [AMBER] ligand is not opening in the binding site of protein muhammad tahir ayub (Fri Dec 11 2015 - 00:22:36 PST)
- [AMBER] WARNING: There is a bond of 420.000806 angstroms between: ------- .R<LIG 546>.A<O2 28> and .R<LIG 546>.A<H2 31> Andrew Bostick (Fri Dec 11 2015 - 07:30:16 PST)
- [AMBER] Problem with initial complex structure for TI Kalenkiewicz, Andrew (NIH/NICHD) [F] (Fri Dec 11 2015 - 15:17:11 PST)
- [AMBER] problem in adding ACE and NME to CSX. Saman Yousuf ali (Sun Dec 13 2015 - 04:58:06 PST)
- [AMBER] RED vIII for Amber Nash, Anthony (Sun Dec 13 2015 - 13:41:19 PST)
- [AMBER] Time Step Wong Li Zhe (Sun Dec 13 2015 - 23:01:18 PST)
- Re: [AMBER] Problems regarding using ZAFF Bill Ross (Sun Dec 13 2015 - 23:01:56 PST)
- [AMBER] restraints on group of atoms Dhananjay (Mon Dec 14 2015 - 01:47:47 PST)
- [AMBER] HBOND_water mediated Lara rajam (Mon Dec 14 2015 - 07:16:58 PST)
- Re: [AMBER] cpptraj grid command Thomas Fox (Mon Dec 14 2015 - 08:24:46 PST)
- [AMBER] MMPBSA.py.MPI compling issue Marc Zhang (Mon Dec 14 2015 - 13:22:14 PST)
- [AMBER] charge fitting procedure in amber conor parks (Mon Dec 14 2015 - 13:27:21 PST)
- [AMBER] Irregular ligand positioning in simulations Anasuya Dighe (Mon Dec 14 2015 - 22:58:43 PST)
- [AMBER] problem in plotting secondary structure graph Sehrish Naz (Mon Dec 14 2015 - 23:19:32 PST)
- [AMBER] confusion in xleap for ligand and comlex Ayesha Kanwal (Mon Dec 14 2015 - 23:50:07 PST)
- [AMBER] mbar Johannes Loeffler (Tue Dec 15 2015 - 05:36:06 PST)
- [AMBER] Warning regarding "triangular bond" Xiong Jiawei (Tue Dec 15 2015 - 23:30:52 PST)
- [AMBER] Ligand's parameterization Trang Nguyen (Wed Dec 16 2015 - 06:07:55 PST)
- [AMBER] Minimization after simulated annealing (0° C) ans CSH script need to be combined V. Kumar (Wed Dec 16 2015 - 09:14:26 PST)
- [AMBER] cpptraj average structure warning George Tzotzos (Thu Dec 17 2015 - 01:05:26 PST)
- [AMBER] Termodinamic Integration setup error Claire Coderch Boué (Thu Dec 17 2015 - 01:46:17 PST)
- [AMBER] Water model jfliu (Thu Dec 17 2015 - 05:07:40 PST)
- [AMBER] How to have special residues in trajectory file using cpptraj shahab shariati (Thu Dec 17 2015 - 06:14:43 PST)
- [AMBER] Confusion on "No Pressure" Robert Molt (Thu Dec 17 2015 - 08:38:13 PST)
- [AMBER] Is triplicate analysis required for pmemd.MPI and ig=-1? Morrow,John Kenneth (Thu Dec 17 2015 - 14:25:51 PST)
- [AMBER] average structure Andrew Bostick (Thu Dec 17 2015 - 14:35:59 PST)
- [AMBER] How to calculate the interplanar angle between 2 Trp residues? Yew Mun Yip (Sun Dec 20 2015 - 01:12:00 PST)
- [AMBER] TIP3 simulated annealing, 200ps*50 loops = 10ns ==> Minimization of lower energy structures V. Kumar (Sun Dec 20 2015 - 04:23:27 PST)
- [AMBER] GPU support Rupak Pal (Sun Dec 20 2015 - 22:51:10 PST)
- [AMBER] pmemd issue Mahmoud A. A. Ibrahim (Mon Dec 21 2015 - 02:04:08 PST)
- [AMBER] ig=-1 for multi production runs Fabian gmail (Mon Dec 21 2015 - 04:31:01 PST)
- [AMBER] Finding PDF of individual dihedral angles Mahendra B Thapa (Mon Dec 21 2015 - 09:27:37 PST)
- [AMBER] TI/MBAR energy re-calculating with imin5 wliu (Wed Dec 23 2015 - 01:16:12 PST)
- [AMBER] MMPBSA error Lara rajam (Wed Dec 23 2015 - 10:05:05 PST)
- [AMBER] A problem about using AMBER 东不拉 (Sun Dec 27 2015 - 21:34:01 PST)
- [AMBER] MD study of transition of protein from one conformation to another Abhilash J (Mon Dec 28 2015 - 09:40:28 PST)
- [AMBER] Group specification Havva Mehralitabar (Mon Dec 28 2015 - 12:52:51 PST)
- [AMBER] different dielectric constant value for polar non-polar hydrophobic residue in MMGBSA bharat lakhani (Tue Dec 29 2015 - 21:47:05 PST)
- [AMBER] which chain to select for MD simulation. Saman Yousuf ali (Wed Dec 30 2015 - 11:58:24 PST)
- [AMBER] Problem in interpreting snapshot_statistics.out after per-residue decomposition analysis Soong Jiaxin (Wed Dec 30 2015 - 19:36:54 PST)
- [AMBER] Error in running AMBER 12 GPU simulations Yogeeshwar Ajjugal (Thu Dec 31 2015 - 05:35:30 PST)
- Last message date: Thu Dec 31 2015 - 08:30:03 PST
- Archived on: Wed Apr 24 2024 - 05:55:15 PDT
