Amber Archive Jan 2016 by thread
- [AMBER] Active site conserve water issue. Saman Yousuf ali (Sat Jan 02 2016 - 05:24:31 PST)
- [AMBER] PMF Rasha Alqus (Sat Jan 02 2016 - 22:34:59 PST)
- [AMBER] Convert gromacs output file to Amber format neha chaudhary (Sun Jan 03 2016 - 00:40:16 PST)
- [AMBER] pH dependent calculation for Oligomers Mijiddorj Batsaikhan (Mon Jan 04 2016 - 02:19:06 PST)
- [AMBER] shape of a peptide array Fabian gmail (Mon Jan 04 2016 - 03:54:34 PST)
- [AMBER] Fwd: Requesting clarifications about QM/MM minimization Manjula Saravanan (Mon Jan 04 2016 - 21:39:25 PST)
- [AMBER] ligand topology genaration neha chaudhary (Tue Jan 05 2016 - 02:24:34 PST)
- [AMBER] Problems with tleap when generating gib structures Levan Tsereteli (Tue Jan 05 2016 - 03:36:32 PST)
- [AMBER] Sander minimization of protein-ligand complex Manjula Saravanan (Tue Jan 05 2016 - 21:21:23 PST)
- [AMBER] xleap : adding ions out of box Himanshu Joshi (Tue Jan 05 2016 - 23:45:48 PST)
- [AMBER] MMPBSA_Error: Could not find necessary program [mmpbsa_py_energy] Pallavi Mohanty (Tue Jan 05 2016 - 23:48:37 PST)
- [AMBER] How to appropriately replace the amber force in the source codes ? jinfeng liu (Wed Jan 06 2016 - 05:37:46 PST)
- [AMBER] Fwd: arrêt de travail Elisa Frezza (Wed Jan 06 2016 - 05:40:06 PST)
- [AMBER] hbond and image problem in cpptraj Chris (Wed Jan 06 2016 - 19:46:03 PST)
- [AMBER] Errors during Building Sidechain Model（MCPB program） 王远强 (Wed Jan 06 2016 - 20:38:31 PST)
- [AMBER] Error in running AMBER 12 GPU simulations[application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0] Yogeeshwar Ajjugal (Wed Jan 06 2016 - 21:43:47 PST)
- [AMBER] Help: parameters of Equilibration and production scripts Sehrish Naz (Wed Jan 06 2016 - 22:05:43 PST)
- [AMBER] how to make active site conserve water unique before loading pdb on xleap? Saman Yousuf ali (Thu Jan 07 2016 - 11:11:36 PST)
- [AMBER] Remove single water molecule using thermodynamic integration Johannes Loeffler (Fri Jan 08 2016 - 00:10:09 PST)
- [AMBER] parmed question regarding modifying Lennard-Jones parameters InSuk Joung (Fri Jan 08 2016 - 00:45:03 PST)
- [AMBER] High RMSD values due to use of iwrap richa anand (Fri Jan 08 2016 - 03:09:12 PST)
- [AMBER] Questions about Steered MD in Amber Vu Truong (Fri Jan 08 2016 - 15:23:36 PST)
- [AMBER] Dr Baliram Lone Dr Baliram lone (Sat Jan 09 2016 - 00:31:38 PST)
- [AMBER] exact values corresponding to the grid points in GIST calculations Mohan Pradhan (Sat Jan 09 2016 - 02:36:25 PST)
- [AMBER] Problem when using lipid14 force filed in Amber 11 Bin Wang (Sat Jan 09 2016 - 14:40:26 PST)
- [AMBER] Scripting CPPTRAJ Analysis Commands within a PBS Script Robert Molt (Sat Jan 09 2016 - 21:12:53 PST)
- [AMBER] premed.MPI warning George Tzotzos (Sun Jan 10 2016 - 02:37:45 PST)
- [AMBER] problem with pmemd.cuda and PBS Indrajit Deb (Mon Jan 11 2016 - 05:52:32 PST)
- [AMBER] MMPBSA Job Parallel Running Guqin Shi (Mon Jan 11 2016 - 11:29:39 PST)
- [AMBER] MCPB Step 2s help Tavenor, Nathan Albert (Mon Jan 11 2016 - 12:30:42 PST)
- [AMBER] Xmgrace Wong Li Zhe (Mon Jan 11 2016 - 18:26:54 PST)
- [AMBER] mmpbsa calculation elham sattarinezhad (Tue Jan 12 2016 - 02:53:53 PST)
- Re: [AMBER] parameters for Mono-methylated Lysine Yin, Guowei (Tue Jan 12 2016 - 11:13:09 PST)
- [AMBER] RMSD selected residues Vertika Gautam (Tue Jan 12 2016 - 23:02:58 PST)
- [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch tarak karmakar (Wed Jan 13 2016 - 05:42:37 PST)
- [AMBER] System becomes unstable upon heating Sudip Das (Wed Jan 13 2016 - 07:19:47 PST)
- [AMBER] Contact analysis using cpptraj Kucharski Jr., Amir N (Wed Jan 13 2016 - 07:25:22 PST)
- [AMBER] Kinetic Energy Wong Li Zhe (Wed Jan 13 2016 - 15:54:50 PST)
- [AMBER] How to maintain planerity of graphene sheets jagannath mondal (Wed Jan 13 2016 - 23:16:34 PST)
- [AMBER] Howto cpptraj - multiple trajin-commands in one line Falko Jähnert (Thu Jan 14 2016 - 04:25:22 PST)
- [AMBER] Problem with A08 tutorial, solvateBox error Elisa Pieri (Thu Jan 14 2016 - 04:41:12 PST)
- [AMBER] Questions about Steered MD in Amber Vu Truong (Thu Jan 14 2016 - 12:10:59 PST)
- [AMBER] contact analysis with CPPTRAJ anu chandra (Fri Jan 15 2016 - 03:59:04 PST)
- [AMBER] Problem installing AmberTools1.5 on Mac OS X 10.11 EL Capitan Ekaterina Ratkova (Fri Jan 15 2016 - 04:15:05 PST)
- [AMBER] Fwd: Problem installing AmberTools1.5 on Mac OS X 10.11 EL Capitan Ekaterina Ratkova (Fri Jan 15 2016 - 04:21:21 PST)
- [AMBER] Problem installing AmberTools1.5 on Mac OS X 10.11 EL Capitan Ratkova, Ekaterina, Dr. (Fri Jan 15 2016 - 04:53:42 PST)
- [AMBER] Angle calculation between two structures anu chandra (Fri Jan 15 2016 - 04:58:21 PST)
- [AMBER] QM/MM/MD simulation zengxitao (Fri Jan 15 2016 - 05:49:17 PST)
- [AMBER] cpptraj question Robert Molt (Sat Jan 16 2016 - 08:38:36 PST)
- [AMBER] Parameter and coordinate files Stefano Sarao S215563 (Sat Jan 16 2016 - 11:12:47 PST)
- [AMBER] format of seconday structure calculation by cpptraj Sangita Kachhap (Sun Jan 17 2016 - 05:26:21 PST)
- [AMBER] Fail to start nab Nikolay N. Kuzmich (Mon Jan 18 2016 - 02:32:53 PST)
- [AMBER] Need Help regarding Energy Calculation Saikat Dutta chowdhury (Mon Jan 18 2016 - 03:57:46 PST)
- [AMBER] python error when using pdb4amber Elisa Pieri (Mon Jan 18 2016 - 04:34:15 PST)
- [AMBER] Problems when trying to improve angle parameters whith paramfit Jérémie KNOOPS [531802] (Mon Jan 18 2016 - 04:45:29 PST)
- [AMBER] Enthalpy of solute+solvent Sergey Samsonov (Mon Jan 18 2016 - 07:12:54 PST)
- [AMBER] Completely fixed atoms in MD Simulation (pmemd) Melisa Averina (Mon Jan 18 2016 - 12:03:36 PST)
- [AMBER] Improving the quality of the model Sushi Shilpa (Tue Jan 19 2016 - 22:50:23 PST)
- [AMBER] problem with reduce and energy minimization Maryam Hamzehee (Wed Jan 20 2016 - 23:55:38 PST)
- [AMBER] Amber14 Installation with cuda יוכבד (Thu Jan 21 2016 - 06:30:12 PST)
- [AMBER] Amber 12 GTX-980 Sarah Graham (Thu Jan 21 2016 - 07:07:48 PST)
- [AMBER] MMPBSA for apo-proteins Kucharski Jr., Amir N (Thu Jan 21 2016 - 10:56:23 PST)
- [AMBER] Problem with Tleap Luis Esteban (Thu Jan 21 2016 - 17:00:47 PST)
- [AMBER] FW: Problem with Tleap Luis Esteban (Thu Jan 21 2016 - 21:07:31 PST)
- [AMBER] MCPB.py error chemjxn (Thu Jan 21 2016 - 22:48:51 PST)
- [AMBER] Stability Calculation using MMPBSA.py Saikat Dutta chowdhury (Fri Jan 22 2016 - 02:08:25 PST)
- [AMBER] Error: A residue defined as a "fast 3-point water" Saman Yousuf ali (Fri Jan 22 2016 - 03:28:34 PST)
- [AMBER] use of LIE command richa anand (Fri Jan 22 2016 - 04:08:06 PST)
- [AMBER] PCA analysis richa anand (Fri Jan 22 2016 - 04:18:53 PST)
- [AMBER] How to put ACE and NME on the ends of a missing loop Elisa Pieri (Fri Jan 22 2016 - 05:20:39 PST)
- [AMBER] KeyError - MCPB.py tutorial David Mayes (Fri Jan 22 2016 - 05:25:07 PST)
- [AMBER] What is the most modern AMBER parm/top format? Christian Schafmeister (Fri Jan 22 2016 - 07:58:31 PST)
- [AMBER] Run your Amber simulations in the cloud with Rescale Sidney Elmer (Fri Jan 22 2016 - 08:45:27 PST)
- [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15 jinfeng liu (Sat Jan 23 2016 - 03:10:34 PST)
- [AMBER] Dear All ankita mehta (Sat Jan 23 2016 - 06:49:59 PST)
- [AMBER] cuda info Carlos Romero (Sat Jan 23 2016 - 22:46:30 PST)
- [AMBER] troubles in understanding, amber minimization input Saman Yousuf ali (Sun Jan 24 2016 - 01:51:32 PST)
- [AMBER] g03 error message Damiano Spadoni (Sun Jan 24 2016 - 10:15:49 PST)
- [AMBER] Running simulations in parallel Aishani Prem (Mon Jan 25 2016 - 10:19:13 PST)
- [AMBER] restraints in simulations Lara rajam (Mon Jan 25 2016 - 10:23:04 PST)
- [AMBER] General question on applying restraints during production MD George Tzotzos (Tue Jan 26 2016 - 02:16:26 PST)
- [AMBER] Question about LJ_1264 for Eu3+? Chris (Tue Jan 26 2016 - 07:15:24 PST)
- [AMBER] Right metal ion model anu chandra (Tue Jan 26 2016 - 08:34:26 PST)
- [AMBER] setup for non-periodic system Covington, Cody Lance (Tue Jan 26 2016 - 13:01:00 PST)
- [AMBER] PCA richa anand (Wed Jan 27 2016 - 01:18:11 PST)
- [AMBER] RMSD w.r.t reference structure richa anand (Wed Jan 27 2016 - 01:24:02 PST)
- [AMBER] 3DRISM: erratic values for partial molar volume Josh Berryman (Wed Jan 27 2016 - 02:05:15 PST)
- [AMBER] two elongated bonds while visualuizing prmtop and inprcd in vmd Nida Baig (Wed Jan 27 2016 - 03:05:38 PST)
- [AMBER] cpptraj molsurf error anu chandra (Wed Jan 27 2016 - 04:23:06 PST)
- [AMBER] atom clash and close contact after MD simulation in water Vasantha Kumar (Wed Jan 27 2016 - 05:50:41 PST)
- [AMBER] free energy calculation of folding Asmita Gupta (Thu Jan 28 2016 - 04:14:33 PST)
- [AMBER] Error Message Wong Li Zhe (Thu Jan 28 2016 - 19:07:41 PST)
- [AMBER] Help to choose best-fit ion model anu chandra (Fri Jan 29 2016 - 06:26:39 PST)
- [AMBER] aMD with two component Khabiri, Morteza (Fri Jan 29 2016 - 10:26:47 PST)
- Last message date: Fri Jan 29 2016 - 15:00:03 PST
- Archived on: Wed Dec 25 2024 - 05:55:18 PST
