Amber Archive Nov 2016 by thread
- [AMBER] mmpbsa error 东不拉 (Tue Nov 01 2016 - 01:31:34 PDT)
- Re: [AMBER] [mdout_analyzer.py] Problem with OS X El Capitan Eiros Zamora, Juan (Tue Nov 01 2016 - 05:59:46 PDT)
- [AMBER] MCPB problems Fabrício Bracht (Tue Nov 01 2016 - 07:58:42 PDT)
- [AMBER] problem with MMPBSApy in Amber 16 Marek Maly (Tue Nov 01 2016 - 08:54:04 PDT)
- [AMBER] The ultimate temperature is 11K instead of 100K in heating simulation Nikolay N. Kuzmich (Tue Nov 01 2016 - 10:34:22 PDT)
- [AMBER] Gromber failed. Dd H (Wed Nov 02 2016 - 01:43:51 PDT)
- [AMBER] Simulation of protein in lipid blayer using GB solvation model Nikolay N. Kuzmich (Wed Nov 02 2016 - 03:49:34 PDT)
- [AMBER] Problem installing Amber 16 on mac OS El Capitan Ruth Helena Tichauer (Wed Nov 02 2016 - 06:32:15 PDT)
- [AMBER] MMGBSA: estimating "effective energy" convergence George Tzotzos (Wed Nov 02 2016 - 06:38:36 PDT)
- Re: [AMBER] Can we combine amber and gaff atom types? Aditya G Rao (Wed Nov 02 2016 - 06:55:12 PDT)
- [AMBER] micro iterations in QM/MM optimization. Yigal Lahav (Wed Nov 02 2016 - 07:28:57 PDT)
- [AMBER] Problem with bonds in NAB Vladislav Sláma (Wed Nov 02 2016 - 08:39:12 PDT)
- [AMBER] Generating parameters of HEME Ramin Ekhteiari (Wed Nov 02 2016 - 10:32:11 PDT)
- [AMBER] How to visualize modes obtained from NMA The Cromicus Productions (Wed Nov 02 2016 - 11:23:30 PDT)
- [AMBER] Software announcement: Release of PUPIL 3.1 Joan Torras (Wed Nov 02 2016 - 13:33:54 PDT)
- [AMBER] Error in the production of heat.rst file Stacyann Nelson (Wed Nov 02 2016 - 17:32:33 PDT)
- Re: [AMBER] MCPB.py Mahmood Jasim (Thu Nov 03 2016 - 03:02:59 PDT)
- [AMBER] RESP routine not found Marcelo Depólo (Thu Nov 03 2016 - 05:09:32 PDT)
- [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Andreas Tosstorff (Thu Nov 03 2016 - 05:15:47 PDT)
- [AMBER] cpptraj error: 'cluster': Command not found. Ruth Helena Tichauer (Thu Nov 03 2016 - 08:59:45 PDT)
- [AMBER] MD simulations, DDR4 2133MHz vs 3200MHz Nikolay N. Kuzmich (Thu Nov 03 2016 - 10:53:17 PDT)
- [AMBER] Failed to install mpirun Nikolay N. Kuzmich (Thu Nov 03 2016 - 10:58:30 PDT)
- [AMBER] Quenstions about pmemd.cuda.MPI Pengfei Li (Thu Nov 03 2016 - 20:20:41 PDT)
- [AMBER] do_debugf changes energy Ulf Ryde (Thu Nov 03 2016 - 23:25:11 PDT)
- [AMBER] Fw:problems for running step 2 of MCPB.py 杨满意 (Fri Nov 04 2016 - 00:00:56 PDT)
- [AMBER] ntt = 6 and ibelly = 1 Xiangyu Jia (Fri Nov 04 2016 - 01:50:03 PDT)
- [AMBER] virtual box in gas phase simulation Xiangyu Jia (Fri Nov 04 2016 - 02:07:25 PDT)
- [AMBER] Umbrella simulation with an arbitrary bias potential diego.soler.uam.es (Fri Nov 04 2016 - 03:02:04 PDT)
- [AMBER] Uridine diphosphate (UDP) - tleap Anna Cebrian Prats (Fri Nov 04 2016 - 04:58:51 PDT)
- [AMBER] RNA backbone dihedral restraints question Kasprzak, Wojciech (NIH/NCI) [C] (Fri Nov 04 2016 - 07:05:25 PDT)
- [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? Eric Lang (Fri Nov 04 2016 - 08:08:55 PDT)
- [AMBER] can not find chamber in amber16? Neale, Christopher Andrew (Fri Nov 04 2016 - 09:25:51 PDT)
- [AMBER] Potential energy fluctuation of NVT ensemble Zhe Li (Fri Nov 04 2016 - 15:15:49 PDT)
- [AMBER] Hello! Distance restraint problems in SANDER tanfei777.sina.cn (Sat Nov 05 2016 - 01:11:18 PDT)
- [AMBER] MM-PBSA calculation for HEME-contained protein Ramin Ekhteiari (Sat Nov 05 2016 - 05:14:47 PDT)
- Re: [AMBER] Ligand across membrane zoran matovic (Sun Nov 06 2016 - 23:38:25 PST)
- [AMBER] enhanced sampling conformations by AMD Kat G (Mon Nov 07 2016 - 09:03:29 PST)
- [AMBER] Performance drop for large systems Andreas Tosstorff (Tue Nov 08 2016 - 02:11:46 PST)
- [AMBER] Coordinates for PEG4K, Folic acid and chitin Abdul Ajees (Tue Nov 08 2016 - 03:02:37 PST)
- [AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped) Michael Shokhen (Tue Nov 08 2016 - 05:28:06 PST)
- [AMBER] Error in running FEW calculations Miguel Rivera (Tue Nov 08 2016 - 12:50:23 PST)
- [AMBER] number of cpus in parallel GPU jobs Neha Gandhi (Tue Nov 08 2016 - 17:42:03 PST)
- [AMBER] AMBER FF for intrinsically disordered protein giulia palermo (Tue Nov 08 2016 - 19:53:35 PST)
- [AMBER] log file in aMD Neha Gandhi (Wed Nov 09 2016 - 02:50:12 PST)
- [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories Eric Lang (Wed Nov 09 2016 - 03:44:02 PST)
- [AMBER] PCA trajectories give unrealistic structures Gulsevin,Alican (Wed Nov 09 2016 - 08:06:43 PST)
- [AMBER] integer limit for nstlim Neale, Christopher Andrew (Wed Nov 09 2016 - 14:14:12 PST)
- [AMBER] compute RESP charges asdda asa (Wed Nov 09 2016 - 14:16:45 PST)
- [AMBER] CUDA version for Amber14 Sofia Vasilakaki (Wed Nov 09 2016 - 14:17:39 PST)
- [AMBER] recompile Sander suite Ibrahim Said (Thu Nov 10 2016 - 02:56:34 PST)
- [AMBER] MCPB.py error in Step 2 Jon Mujika (Thu Nov 10 2016 - 03:25:11 PST)
- [AMBER] Constant pH charge set Fabrício Bracht (Thu Nov 10 2016 - 06:05:42 PST)
- [AMBER] Parameters for selenocysteine Paul Meister (Thu Nov 10 2016 - 06:06:54 PST)
- [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB Ruth Helena Tichauer (Thu Nov 10 2016 - 06:07:29 PST)
- [AMBER] Problem with Parmed-generated chamber prmtop Marc van der Kamp (Thu Nov 10 2016 - 07:01:48 PST)
- [AMBER] ambmask issue Aseel Bala (Thu Nov 10 2016 - 15:08:01 PST)
- [AMBER] cpptraj: RMSD vs Residue Number. Saman Yousuf ali (Fri Nov 11 2016 - 00:48:23 PST)
- [AMBER] GIST: convergence of the translational entropy term Sergey Samsonov (Fri Nov 11 2016 - 06:28:26 PST)
- [AMBER] Constraints Ol Sta (Fri Nov 11 2016 - 06:34:07 PST)
- [AMBER] NPT equilibration at constant pH with protonation states allowed to change Eric Lang (Fri Nov 11 2016 - 09:31:56 PST)
- [AMBER] length of restraintmask Ignacio J. General (Fri Nov 11 2016 - 09:51:50 PST)
- [AMBER] MMGBSA decomposition analysis George Tzotzos (Fri Nov 11 2016 - 13:16:41 PST)
- [AMBER] error in antechamber Nehad Elsalamouny (Fri Nov 11 2016 - 16:10:17 PST)
- [AMBER] Query regarding the MCPB.py workflow Abhi Acharya (Sat Nov 12 2016 - 01:09:19 PST)
- [AMBER] Generation of parameter files of transmembrane protein system via xleap Mahrukh Imtiaz (Mon Nov 14 2016 - 01:05:39 PST)
- [AMBER] dlpc membrane jojartb.jgypk.u-szeged.hu (Mon Nov 14 2016 - 01:45:03 PST)
- [AMBER] Targeted molecular dynamics on GPU Sonia Ziada (Mon Nov 14 2016 - 07:14:34 PST)
- [AMBER] how to neutralize protein when using intrinsic water model Thakur, Abhishek (Mon Nov 14 2016 - 08:00:46 PST)
- [AMBER] Filename being truncated by pmemd.cuda Andreas Tosstorff (Mon Nov 14 2016 - 08:14:03 PST)
- [AMBER] covalently bound ligand Ahsan Mohd (Mon Nov 14 2016 - 10:20:14 PST)
- Re: [AMBER] Negative interaction energy between Sodium ions? Oliver Emil Skytte Glue (Mon Nov 14 2016 - 14:29:17 PST)
- [AMBER] Restraints not working, What Am I doing Wrong? The Cromicus Productions (Mon Nov 14 2016 - 23:28:17 PST)
- [AMBER] Methylated adenine parameter Kshatresh Dutta Dubey (Tue Nov 15 2016 - 02:45:07 PST)
- [AMBER] simulating with "gbsa=1" on gpu give only 0.18ns per/day Thakur, Abhishek (Tue Nov 15 2016 - 07:01:41 PST)
- [AMBER] Compatibility of Amber parameters for FF99 and FF14SB forcefields DmitryASuplatov (Tue Nov 15 2016 - 08:12:45 PST)
- [AMBER] Help Constant pH MD calculations Tsibela German Tebello Mofokeng (Tue Nov 15 2016 - 08:32:45 PST)
- [AMBER] Energy decomposition of free energy profiles wjli (Tue Nov 15 2016 - 17:46:53 PST)
- Re: [AMBER] MD simulation by amber Hai Nguyen (Tue Nov 15 2016 - 18:40:12 PST)
- Re: [AMBER] mm_pbsa.pl error: Found unknown atflg DC Hai Nguyen (Tue Nov 15 2016 - 18:42:37 PST)
- [AMBER] MM-GBSA calculation in temperature other than 298.15 K Atila Petrosian (Tue Nov 15 2016 - 21:42:37 PST)
- [AMBER] GaMD patches to Amber 14 and PME's gridhi parameter Kasprzak, Wojciech (NIH/NCI) [C] (Wed Nov 16 2016 - 06:07:03 PST)
- [AMBER] HMassRepartition Thakur, Abhishek (Wed Nov 16 2016 - 07:38:23 PST)
- [AMBER] compatibility Magno . (Wed Nov 16 2016 - 10:13:16 PST)
- [AMBER] MD under external electric field Hector A. Baldoni (Wed Nov 16 2016 - 13:36:05 PST)
- [AMBER] ATP Parameters for ff14SB Stevens, David Ryan (Wed Nov 16 2016 - 13:57:21 PST)
- [AMBER] cpptraj RMSD calculation with mismatch residue numbers anu chandra (Wed Nov 16 2016 - 15:02:04 PST)
- [AMBER] Phosphoryated amino acids Beale, John (Thu Nov 17 2016 - 01:10:30 PST)
- [AMBER] No output_file during SMD with LCOD Ruth Helena Tichauer (Thu Nov 17 2016 - 02:45:47 PST)
- [AMBER] Converting coordinate file generated into pdb format for nuparm ABHIJEET CHOWDHURY (Thu Nov 17 2016 - 04:43:59 PST)
- [AMBER] Fwd: Normal Mode Analysis Imma Speciale (Thu Nov 17 2016 - 05:47:45 PST)
- [AMBER] creating parameters for integrins Tsibela German Tebello Mofokeng (Thu Nov 17 2016 - 09:22:03 PST)
- [AMBER] ImportError: Could not import Amber Python modules Thakur, Abhishek (Thu Nov 17 2016 - 09:42:56 PST)
- [AMBER] ambmask issue Aseel Bala (Thu Nov 17 2016 - 10:21:11 PST)
- [AMBER] extracting velocities from rst7 file giulia palermo (Thu Nov 17 2016 - 10:55:59 PST)
- [AMBER] Issue with addAtomType: Syntax Error Korey M Reid (Thu Nov 17 2016 - 12:14:36 PST)
- [AMBER] strange format of .rst file Thakur, Abhishek (Fri Nov 18 2016 - 07:53:41 PST)
- [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) The Cromicus Productions (Fri Nov 18 2016 - 10:26:21 PST)
- [AMBER] Converting a PDB Collection to a NetCDF trajectory Dmitry Suplatov (Fri Nov 18 2016 - 12:11:41 PST)
- [AMBER] generated correct inputfiles(.iprmtop and .inpcrd ) files 杨满意 (Fri Nov 18 2016 - 19:12:20 PST)
- [AMBER] TUTORIAL B5: Simulating the Green Fluorescent Protein -PREPGEN Error Taylor, Miles (Sat Nov 19 2016 - 16:50:20 PST)
- [AMBER] How to change the dielectric constant in the electrostatic energy term? 冯国强 (Sun Nov 20 2016 - 08:02:05 PST)
- [AMBER] The parameters for the fully protonated phosphate group jinfeng liu (Sun Nov 20 2016 - 18:45:31 PST)
- [AMBER] MMPBSA Calculation Preeti Pandey (Mon Nov 21 2016 - 08:49:43 PST)
- [AMBER] Lifetime Analysis in cpptraj MOHD HOMAIDUR RAHMAN (Mon Nov 21 2016 - 11:20:06 PST)
- [AMBER] Convert prm into prmtop - from NAMD to AMBER The Cromicus Productions (Mon Nov 21 2016 - 11:21:43 PST)
- [AMBER] cap the 5' phosphate of a RNA Mohaddeseh Habibzadeh (Mon Nov 21 2016 - 11:48:23 PST)
- [AMBER] 20161121141138.GE88784.scarletmail.rutgers.edu Taylor, Miles (Mon Nov 21 2016 - 12:36:36 PST)
- [AMBER] implicit water model in aMD Thakur, Abhishek (Mon Nov 21 2016 - 13:45:04 PST)
- [AMBER] creating 5' phosphate groups David A Case (Mon Nov 21 2016 - 14:36:13 PST)
- [AMBER] [Amber] Calculating Normal Modes with Restrictions The Cromicus Productions (Mon Nov 21 2016 - 17:00:26 PST)
- Re: [AMBER] AMBER Digest, Vol 1763, Issue 1 冯国强 (Tue Nov 22 2016 - 00:52:41 PST)
- [AMBER] Protein path error Arthi Venkat (Tue Nov 22 2016 - 01:52:18 PST)
- [AMBER] Modes associated to the principal components? The Cromicus Productions (Tue Nov 22 2016 - 06:54:45 PST)
- [AMBER] Could not find enough velocities in .rst Ruth Helena Tichauer (Tue Nov 22 2016 - 09:21:32 PST)
- [AMBER] DIfferences between thermostats Markowska (Tue Nov 22 2016 - 11:31:18 PST)
- [AMBER] is it possible to run aMD in implicit water model? Thakur, Abhishek (Tue Nov 22 2016 - 12:51:26 PST)
- [AMBER] Paramfit for multiple molecules Sven Hackbusch (Tue Nov 22 2016 - 15:59:22 PST)
- [AMBER] How to generated correct inputfiles(.iprmtop and .inpcrd ) files 杨满意 (Tue Nov 22 2016 - 17:11:13 PST)
- [AMBER] simulation running error. Saman Yousuf ali (Tue Nov 22 2016 - 21:31:15 PST)
- [AMBER] rmsf problem Sepideh Jafari (Wed Nov 23 2016 - 02:07:27 PST)
- [AMBER] Error, charge not integral Fabrício Bracht (Wed Nov 23 2016 - 02:26:46 PST)
- [AMBER] aMD with dt=0.004 Thakur, Abhishek (Wed Nov 23 2016 - 06:53:34 PST)
- [AMBER] About multiconformations RESP fitting Marion, Antoine (Wed Nov 23 2016 - 07:39:16 PST)
- [AMBER] 20161121141138.GE88784.scarletmail.rutgers.edu Taylor, Miles (Wed Nov 23 2016 - 07:56:48 PST)
- [AMBER] more on the Berendsen thermostat David A Case (Wed Nov 23 2016 - 10:44:29 PST)
- [AMBER] Hydrophobic and covalent interactions bond length and stability muhammad tahir ayub (Wed Nov 23 2016 - 21:46:04 PST)
- Re: [AMBER] Distorsion in water box size and shape Mahrukh Imtiaz (Wed Nov 23 2016 - 22:13:14 PST)
- [AMBER] Optimal values for harm and output_freq in SMD Ruth Helena Tichauer (Thu Nov 24 2016 - 03:34:04 PST)
- [AMBER] GlcNAc-UDP problem with frcmod file Sonia Romero (Fri Nov 25 2016 - 02:15:41 PST)
- [AMBER] Problem to submit a pH-REMD on a GPU node Yong Wang (Fri Nov 25 2016 - 02:54:49 PST)
- [AMBER] Extract temperature of a subsytem diego.soler.uam.es (Fri Nov 25 2016 - 03:22:15 PST)
- [AMBER] Dynamic at high temperature Imma Speciale (Fri Nov 25 2016 - 03:49:01 PST)
- Re: [AMBER] Wierd line in amber-TI output Files Thomas Fox (Fri Nov 25 2016 - 04:37:22 PST)
- [AMBER] instal aamber "mpich2" Sepideh Jafari (Fri Nov 25 2016 - 09:23:44 PST)
- [AMBER] Tools for calculation of interaction energy Andrew Bostick (Fri Nov 25 2016 - 09:41:26 PST)
- [AMBER] Convert mdcrd files into pbd files The Cromicus Productions (Fri Nov 25 2016 - 14:47:00 PST)
- [AMBER] Obtaining infrared/Raman spectra The Cromicus Productions (Sat Nov 26 2016 - 00:36:22 PST)
- [AMBER] MCPB.py and MMPBSA issue 庄灿波 (Sat Nov 26 2016 - 01:32:53 PST)
- [AMBER] recipe for target "parallel" failed Mohaddeseh Habibzadeh (Sat Nov 26 2016 - 10:08:58 PST)
- [AMBER] How to create the .off/.lib file of the equilibrated non-aqueous solvent box? Yew Mun Yip (Sat Nov 26 2016 - 22:05:12 PST)
- [AMBER] NAB input file containing first and second structure of RNA Mohaddeseh Habibzadeh (Sat Nov 26 2016 - 22:56:16 PST)
- [AMBER] Regarding integration of my code with CPPTRAJ Nikhil Chowdary (Sun Nov 27 2016 - 21:35:46 PST)
- [AMBER] AMBER Materials modelling- periodic image Neha Gandhi (Sun Nov 27 2016 - 21:41:46 PST)
- [AMBER] cudaMemcpyToSymbol Error cuiyinglukitty (Mon Nov 28 2016 - 00:45:48 PST)
- [AMBER] Questions concerning charges calculated by antechamber Andreas Gavrielides (Mon Nov 28 2016 - 04:36:19 PST)
- [AMBER] solvate box of long length and short width Lara rajam (Mon Nov 28 2016 - 06:58:31 PST)
- [AMBER] Etot = ************** with dtt=0.004 Thakur, Abhishek (Mon Nov 28 2016 - 08:29:40 PST)
- [AMBER] MM-GBSA calculation in temperature other than 298 K Atila Petrosian (Mon Nov 28 2016 - 10:47:36 PST)
- [AMBER] RMSD for two different MDs Haining Liu (Mon Nov 28 2016 - 12:49:02 PST)
- [AMBER] Fw: Problems with imaging Mark Waterhouse [RPG] (Mon Nov 28 2016 - 12:49:09 PST)
- [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Brian Radak (Tue Nov 29 2016 - 10:24:05 PST)
- [AMBER] Error for copper atom type Shreeramesh (Tue Nov 29 2016 - 18:26:02 PST)
- [AMBER] Force field files for ff99IDPs barsha bharadwaz (Wed Nov 30 2016 - 05:04:49 PST)
- [AMBER] Issue with the gaff parameters for "nh" atom type Prajwal Nandekar (Wed Nov 30 2016 - 05:58:45 PST)
- [AMBER] question about calculated density in sander output file amaury paquet (Wed Nov 30 2016 - 06:22:01 PST)
- [AMBER] selection of the residues when using MM-GBSA Hyun (Wed Nov 30 2016 - 08:38:08 PST)
- [AMBER] mdfil: Error unknown flag: pdb_wat.prmtop Aishani Prem (Wed Nov 30 2016 - 15:32:29 PST)
- Last message date: Wed Nov 30 2016 - 16:00:03 PST
- Archived on: Wed Dec 25 2024 - 05:55:27 PST
