Amber Archive Sep 2015 by thread
- Re: [AMBER] Non-equilibrium pulling with plane-point restraints achim.sandmann.chemie.stud.uni-erlangen.de (Tue Sep 01 2015 - 05:42:07 PDT)
- [AMBER] MMPBSA error - start frame (1) > total frames (0) Sangeetha B (Tue Sep 01 2015 - 08:39:44 PDT)
- [AMBER] KeyError: 4018 Sushi Shilpa (Tue Sep 01 2015 - 20:42:09 PDT)
- [AMBER] lifetime analysis loic etheve (Wed Sep 02 2015 - 06:37:45 PDT)
- [AMBER] lifetime analysis loic etheve (Wed Sep 02 2015 - 06:41:46 PDT)
- [AMBER] Amber14 Update 13 fails. Oliver Grant (Wed Sep 02 2015 - 07:44:51 PDT)
- [AMBER] error in GPU during equilibration Lara rajam (Wed Sep 02 2015 - 09:30:26 PDT)
- [AMBER] Different result before and after AUTOIMAGE from CPPTRAJ? Eg eh (Wed Sep 02 2015 - 13:21:50 PDT)
- Re: [AMBER] job submission in RED FyD (Thu Sep 03 2015 - 02:12:10 PDT)
- Re: [AMBER] hpc error Damiano Spadoni (Thu Sep 03 2015 - 03:16:19 PDT)
- [AMBER] RESP charge fitting CHAMI F. (Thu Sep 03 2015 - 11:10:49 PDT)
- [AMBER] Trouble running Thermodynamic Integration in Amber14 with pmemd. Timothy Christopher Schutt (Thu Sep 03 2015 - 15:04:26 PDT)
- [AMBER] MMPBSA error sunita gupta (Fri Sep 04 2015 - 00:12:49 PDT)
- [AMBER] mmpbsa with Iodine problems 21428087.zju.edu.cn (Fri Sep 04 2015 - 21:48:29 PDT)
- [AMBER] gpu run Lara rajam (Sat Sep 05 2015 - 16:32:13 PDT)
- [AMBER] MMPBSA is not performing Asma Abro 28-FBAS/MSBI/F09 (Sun Sep 06 2015 - 22:03:23 PDT)
- [AMBER] Multiplicity in QM/MM calculations Kshatresh Dutta Dubey (Mon Sep 07 2015 - 10:13:38 PDT)
- [AMBER] Parameters for benzene sulfonamide Jovanovic, Srdan (Mon Sep 07 2015 - 10:16:55 PDT)
- Re: [AMBER] closest command in cpptraj Joseph Baker (Mon Sep 07 2015 - 11:22:57 PDT)
- Re: [AMBER] Regarding AmberTool 14 installation Setyanto Md (Mon Sep 07 2015 - 22:03:50 PDT)
- [AMBER] REMD to sample the conformational space of a defined part of the system Sergey Samsonov (Tue Sep 08 2015 - 00:50:33 PDT)
- [AMBER] Amber15 compiler error 'undefined reference to `fftw_plan_dft_r2c_3d'' with Cygwin Nigel Palmer (Tue Sep 08 2015 - 06:16:29 PDT)
- [AMBER] index and sort order in prmtop Hannes Loeffler (Tue Sep 08 2015 - 07:55:06 PDT)
- [AMBER] watershell cpptraj question Travis Hughes (Tue Sep 08 2015 - 08:08:37 PDT)
- [AMBER] Problem compiling cpptraj with openmp Marc van der Kamp (Tue Sep 08 2015 - 08:32:51 PDT)
- [AMBER] ParmEd problem: LJ12_6_4Error: Could not find parameters for ATOM_TYPE CX Karolina Markowska (Tue Sep 08 2015 - 14:41:10 PDT)
- [AMBER] Fw: important Do Yong Kim (Wed Sep 09 2015 - 00:06:23 PDT)
- [AMBER] Contact map residues Neha Gandhi (Wed Sep 09 2015 - 00:30:30 PDT)
- [AMBER] Cphmd Arjun Sharma (Wed Sep 09 2015 - 08:17:13 PDT)
- [AMBER] Changing font size with mdout_analyzer.py Krantzman, Kristin D (Wed Sep 09 2015 - 08:19:31 PDT)
- [AMBER] [parmed.py] chemistry.exceptions.AmberParmError loading topology file Eiros Zamora, Juan (Wed Sep 09 2015 - 10:34:50 PDT)
- [AMBER] QM/MM Equilibration Errors Brittany Boykin (Wed Sep 09 2015 - 14:41:55 PDT)
- [AMBER] cpptraj script for average 3D protein structure? Michael Shokhen (Thu Sep 10 2015 - 01:23:13 PDT)
- [AMBER] several peptides in my input can be identified by cpptraj? Fabian gmail (Thu Sep 10 2015 - 03:05:50 PDT)
- [AMBER] xmgrace in microsoft Martina Devi (Thu Sep 10 2015 - 06:03:09 PDT)
- [AMBER] pca Lara rajam (Thu Sep 10 2015 - 08:30:44 PDT)
- [AMBER] setting a box mohammad r (Thu Sep 10 2015 - 08:35:07 PDT)
- [AMBER] HPC Sofia Vasilakaki (Thu Sep 10 2015 - 12:17:43 PDT)
- [AMBER] MCPB problem Kshatresh Dutta Dubey (Thu Sep 10 2015 - 13:25:00 PDT)
- [AMBER] keep residue numbering? Albert (Fri Sep 11 2015 - 00:12:24 PDT)
- [AMBER] limit exceeded and high temperature Ruth Helena Tichauer (Fri Sep 11 2015 - 07:52:05 PDT)
- [AMBER] Parameterization empirical method Marcelo Andrade Chagas (Fri Sep 11 2015 - 11:40:41 PDT)
- [AMBER] Addition of single water molecules Eric Berquist (Fri Sep 11 2015 - 13:21:06 PDT)
- [AMBER] CpHMD of Succinic Acid Rahul Ramesh (Fri Sep 11 2015 - 18:02:24 PDT)
- [AMBER] FW: No output Damiano Spadoni (Sat Sep 12 2015 - 13:52:00 PDT)
- [AMBER] Testing the mail server George Tzotzos (Sun Sep 13 2015 - 14:51:27 PDT)
- [AMBER] Proper Insertion of Covalently Bound Unit in Helical Structure Robert Molt (Sun Sep 13 2015 - 17:06:36 PDT)
- [AMBER] What is wrong with the minimization? Huggins, Esther, C (Sun Sep 13 2015 - 17:30:50 PDT)
- [AMBER] Simulation stops without errors Bala subramanian (Mon Sep 14 2015 - 00:46:49 PDT)
- [AMBER] Paramfit issues David Poole (Mon Sep 14 2015 - 03:31:57 PDT)
- [AMBER] Parmed crash Mykola Dimura (Mon Sep 14 2015 - 08:50:12 PDT)
- [AMBER] mmpbsa error Lara rajam (Mon Sep 14 2015 - 18:40:49 PDT)
- [AMBER] Regarding Simulations of Ionic Liquids on GPU MOHD HOMAIDUR RAHMAN (Mon Sep 14 2015 - 22:45:41 PDT)
- [AMBER] A question on binding free energy decomposition output wliu (Mon Sep 14 2015 - 23:22:27 PDT)
- [AMBER] query ankita mehta (Tue Sep 15 2015 - 06:22:01 PDT)
- [AMBER] sqm Sofia Vasilakaki (Tue Sep 15 2015 - 07:11:40 PDT)
- [AMBER] Has anyone tried VMD in the second step of tutorial A1? Xing (Tue Sep 15 2015 - 08:52:33 PDT)
- [AMBER] vlimit exceeded and high temperature Ruth Helena Tichauer (Tue Sep 15 2015 - 09:06:34 PDT)
- [AMBER] cyclic peptides and bond command in leap Jonathan Gough (Tue Sep 15 2015 - 10:04:18 PDT)
- [AMBER] Antechamber error Kalenkiewicz, Andrew (NIH/NICHD) [F] (Tue Sep 15 2015 - 11:38:43 PDT)
- [AMBER] Fwd: Mail ceased to work in the last 72 hours George Tzotzos (Tue Sep 15 2015 - 19:01:37 PDT)
- [AMBER] problem in plotting secondary structure graph Sehrish Naz (Tue Sep 15 2015 - 21:11:19 PDT)
- [AMBER] Problems with the Amber-14 compilation and using MMPBSA.py with ubuntu ayesha kanwal (Tue Sep 15 2015 - 23:10:16 PDT)
- [AMBER] help in parallel run Robin Jain (Wed Sep 16 2015 - 02:36:36 PDT)
- [AMBER] Test George Tzotzos (Wed Sep 16 2015 - 05:18:31 PDT)
- [AMBER] cphmd reference energy Arjun Sharma (Wed Sep 16 2015 - 07:44:10 PDT)
- [AMBER] Splitting LES trajectory Sergey Samsonov (Wed Sep 16 2015 - 08:29:52 PDT)
- [AMBER] DISAVE does not work on pmemd.cuda / GPU Mykola Dimura (Wed Sep 16 2015 - 09:57:33 PDT)
- [AMBER] Michaelis complex Hector A. Baldoni (Wed Sep 16 2015 - 13:11:06 PDT)
- [AMBER] Leap Connection of Covalent Unit Continued Robert Molt (Wed Sep 16 2015 - 18:30:45 PDT)
- [AMBER] antechamber error Atila Petrosian (Thu Sep 17 2015 - 06:51:03 PDT)
- [AMBER] Issues with gaff cd=cc atom type Francesco Pietra (Fri Sep 18 2015 - 00:46:20 PDT)
- [AMBER] MG ions being misplaced Kalenkiewicz, Andrew (NIH/NICHD) [F] (Fri Sep 18 2015 - 09:44:27 PDT)
- [AMBER] Molecular Dynamics for Porphyrin Amber Maharaj (Fri Sep 18 2015 - 09:45:47 PDT)
- [AMBER] per residue decomposition MMPBSA Lara rajam (Fri Sep 18 2015 - 10:03:29 PDT)
- [AMBER] CpHMD for non protein residues Rahul Ramesh (Fri Sep 18 2015 - 13:59:29 PDT)
- [AMBER] Minimization Marcelo Andrade Chagas (Fri Sep 18 2015 - 14:13:25 PDT)
- [AMBER] Calculating energy of solute Krantzman, Kristin D (Fri Sep 18 2015 - 14:33:10 PDT)
- [AMBER] Antechamber Flags Robert Molt (Fri Sep 18 2015 - 18:00:04 PDT)
- [AMBER] ambertools14 Andrew Bostick (Sat Sep 19 2015 - 04:30:55 PDT)
- [AMBER] q4md FF with two "small" molecules Francesco Pietra (Sun Sep 20 2015 - 02:01:08 PDT)
- [AMBER] on MD and Ramachandran outlier Brett (Sun Sep 20 2015 - 04:49:12 PDT)
- [AMBER] Extracting Information for each Frames Considered for Entropy Calculation by Normal Modes anilkumarsahoo.physics.iisc.ernet.in (Sun Sep 20 2015 - 15:09:22 PDT)
- [AMBER] QM&Lipid14 Sofia Vasilakaki (Sun Sep 20 2015 - 16:58:28 PDT)
- [AMBER] SHAKE&Vlimit 罗艳玲 (Sun Sep 20 2015 - 18:56:30 PDT)
- [AMBER] Problem In Performing MMPBSA Calculation for System containing Ligand and Protein 杨川 (Sun Sep 20 2015 - 21:30:38 PDT)
- [AMBER] glycam parameter file Batuhan Kav (Mon Sep 21 2015 - 03:23:39 PDT)
- [AMBER] warning when using cpptraj on BB atoms missing Fabian gmail (Mon Sep 21 2015 - 07:16:43 PDT)
- [AMBER] Prospective research areas of AMBER Sabyasachi Sahoo (Mon Sep 21 2015 - 10:25:23 PDT)
- [AMBER] Freeze atoms to DM Marcelo Andrade Chagas (Mon Sep 21 2015 - 12:21:27 PDT)
- [AMBER] Prepgen Robert Molt (Mon Sep 21 2015 - 18:36:43 PDT)
- [AMBER] Installing AMBER Wong Li Zhe (Mon Sep 21 2015 - 20:19:54 PDT)
- [AMBER] distance based mask problem Chris (Mon Sep 21 2015 - 21:01:19 PDT)
- [AMBER] Usage of off-diagonal coupling parameters for EVB model bijyalaxmi athokpam (Tue Sep 22 2015 - 00:38:17 PDT)
- [AMBER] help in RDF Robin Jain (Tue Sep 22 2015 - 01:18:57 PDT)
- [AMBER] Protein - RNA modelling Sidhu, Khushwant (Dr.) (Tue Sep 22 2015 - 06:50:01 PDT)
- [AMBER] degraded GPU performance Alessandro Contini (alessandro.contini) (Tue Sep 22 2015 - 07:22:00 PDT)
- [AMBER] R: Re: degraded GPU performance Alessandro Contini (Tue Sep 22 2015 - 07:50:08 PDT)
- [AMBER] Addions Na+ Marcelo Andrade Chagas (Tue Sep 22 2015 - 11:52:44 PDT)
- [AMBER] AMBER Tutorial B1 Backbone atoms Aishani Prem (Tue Sep 22 2015 - 13:32:28 PDT)
- [AMBER] Halogen bond force field in AMBER psu4.uic.edu (Tue Sep 22 2015 - 15:49:39 PDT)
- [AMBER] OpenMM Sofia Vasilakaki (Tue Sep 22 2015 - 17:26:45 PDT)
- [AMBER] Implementation of GBSA in AMBER. Abhilash J (Tue Sep 22 2015 - 22:14:07 PDT)
- [AMBER] Command for hbond analysis Martina Devi (Wed Sep 23 2015 - 00:41:35 PDT)
- [AMBER] HELP in Emperical Valence bond model (EVB) bijyalaxmi athokpam (Wed Sep 23 2015 - 01:55:54 PDT)
- [AMBER] Hoogsteen-Watson Base pair Martina Devi (Wed Sep 23 2015 - 08:02:01 PDT)
- [AMBER] CpHMD simulation for non protein residues Rahul Ramesh (Wed Sep 23 2015 - 09:05:46 PDT)
- [AMBER] analysis from mixed amber 12 and amber 14 simulations George Green (Wed Sep 23 2015 - 12:22:24 PDT)
- [AMBER] free -COOH at the C-terminus Xing (Thu Sep 24 2015 - 12:11:27 PDT)
- [AMBER] Membrane simulation without a membrane, only lipophilic solvent (membranemimetic) Marawan Hussien (Thu Sep 24 2015 - 18:10:50 PDT)
- [AMBER] Membrane simulation without a membrane, only lipophilic solvent (membranemimetic) sridhar ganesan (Thu Sep 24 2015 - 20:10:43 PDT)
- [AMBER] AMBER benchmarks Neha Gandhi (Fri Sep 25 2015 - 03:05:55 PDT)
- [AMBER] jfastw=4 and vlimit exceeded Ruth Helena Tichauer (Fri Sep 25 2015 - 06:46:06 PDT)
- [AMBER] adQMMM multiple solvation regions Covington, Cody Lance (Fri Sep 25 2015 - 08:03:31 PDT)
- [AMBER] T-REMD Reproducibility - Cluster v.s Desktop Thiago Lipinski Paes (Fri Sep 25 2015 - 09:11:55 PDT)
- [AMBER] Minimization of steps Marcelo Andrade Chagas (Fri Sep 25 2015 - 11:26:39 PDT)
- [AMBER] Fwd: ISC-2015-3BS-09 Sushi Shilpa (Sat Sep 26 2015 - 03:39:40 PDT)
- [AMBER] wrap problem with QM/MM Covington, Cody Lance (Sun Sep 27 2015 - 13:49:38 PDT)
- [AMBER] Problem with saving parameters for a complex having Heme group 杨川 (Sun Sep 27 2015 - 21:29:35 PDT)
- Re: [AMBER] clustering in PC subspace filip fratev (Mon Sep 28 2015 - 15:41:59 PDT)
- [AMBER] Updates for PBSA energy calculations Christina Berti (Mon Sep 28 2015 - 16:17:04 PDT)
- [AMBER] 12 PhD positions for the Marie Skłodowska-Curie ITN-European MoGglyNet Alessandro Contini (Tue Sep 29 2015 - 02:23:46 PDT)
- [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal (Tue Sep 29 2015 - 15:07:43 PDT)
- [AMBER] Amber compilation problem Weinzierl, Robert O J (Wed Sep 30 2015 - 04:43:54 PDT)
- [AMBER] Need help regarding references Saikat Dutta chowdhury (Wed Sep 30 2015 - 05:42:07 PDT)
- [AMBER] Oxygen parameters for AMBER99SB-ILDN Ebert Maximilian (Wed Sep 30 2015 - 10:04:27 PDT)
- Last message date: Wed Sep 30 2015 - 15:30:03 PDT
- Archived on: Fri Apr 19 2024 - 05:55:00 PDT
