Amber Archive Jul 2017 by thread
- [AMBER] error with MMPBSA Mohammad Salem (Fri Jun 30 2017 - 21:22:54 PDT)
- Re: [AMBER] amber installations error in cygwin Hai Nguyen (Sat Jul 01 2017 - 09:04:46 PDT)
- [AMBER] Principal component analysis with CPPTRAJ - PCA Marcelo Andrade Chagas (Sat Jul 01 2017 - 10:40:16 PDT)
- [AMBER] amber error Rana Rehan Khalid (Sat Jul 01 2017 - 13:08:13 PDT)
- Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Sat Jul 01 2017 - 17:47:52 PDT)
- [AMBER] Construction of a large non-standard residue Andrew Schaub (Sat Jul 01 2017 - 17:52:55 PDT)
- [AMBER] MMPBSA maxitn warning with protein/dna complex Baker, Joseph (Sat Jul 01 2017 - 19:19:07 PDT)
- [AMBER] Frcmod and prepin from inpcrd Hirdesh Kumar (Sat Jul 01 2017 - 20:43:17 PDT)
- [AMBER] questions on MMPBSA giulia palermo (Sun Jul 02 2017 - 10:51:21 PDT)
- [AMBER] how can i remove this error Rana Rehan Khalid (Sun Jul 02 2017 - 13:53:15 PDT)
- [AMBER] Problem in cuda for AMBER 14 Mahendra B Thapa (Sun Jul 02 2017 - 19:09:31 PDT)
- Re: [AMBER] FW: Problem in cuda for AMBER 14 Mahendra B Thapa (Sun Jul 02 2017 - 19:30:52 PDT)
- [AMBER] abmer error Rana Rehan Khalid (Sun Jul 02 2017 - 20:57:43 PDT)
- [AMBER] using PCA to find entropy Ramin Salimi (Sun Jul 02 2017 - 23:06:54 PDT)
- Re: [AMBER] error running mmpbsa Elvis Martis (Sun Jul 02 2017 - 23:41:39 PDT)
- Re: [AMBER] TI/FEP on GPU in Amber? liu junjun (Mon Jul 03 2017 - 01:41:16 PDT)
- [AMBER] QM/MM with Gaussian Xichong Liu (Mon Jul 03 2017 - 02:24:38 PDT)
- [AMBER] How continue a crached minimization step? Núbia Prates (Mon Jul 03 2017 - 07:38:34 PDT)
- [AMBER] Selecting solvationBox size to simulate a mobile multidomain protein Dmitry Suplatov (Mon Jul 03 2017 - 11:32:49 PDT)
- Re: [AMBER] Error with 'surf' and acetonitrile-water solvent mixture Daniel Roe (Mon Jul 03 2017 - 12:14:26 PDT)
- [AMBER] xleap editor Rana Rehan Khalid (Mon Jul 03 2017 - 21:42:46 PDT)
- [AMBER] Question about installing Amber16 on the intel Xeon phi computational server Mingyuan (Mon Jul 03 2017 - 23:44:32 PDT)
- [AMBER] Amber md in HPC Garima Singh (Mon Jul 03 2017 - 23:53:42 PDT)
- [AMBER] MPI error when trying to run heating Daniela Rivas (Tue Jul 04 2017 - 03:34:27 PDT)
- [AMBER] MCPB.py error step 2 Lizelle Lubbe (Tue Jul 04 2017 - 04:05:55 PDT)
- [AMBER] Reproduction of MMPBSA Calculations on Processed Trajectories Guqin Shi (Tue Jul 04 2017 - 06:17:33 PDT)
- [AMBER] Residue number in tleap not appropriate with residue number in pdb file NADIA RAHMAH (Tue Jul 04 2017 - 08:00:44 PDT)
- [AMBER] RED ESP not working in these days Rana Rehan Khalid (Tue Jul 04 2017 - 10:23:42 PDT)
- [AMBER] pull a dimer apart in AMBER? Xing (Tue Jul 04 2017 - 19:24:12 PDT)
- [AMBER] Osmotic Pressure Calculation in AMBER Xiaocong Wang (Tue Jul 04 2017 - 20:27:17 PDT)
- [AMBER] MCPB.py error Rana Rehan Khalid (Tue Jul 04 2017 - 20:32:38 PDT)
- [AMBER] icc version 17 Fabrício Bracht (Tue Jul 04 2017 - 20:41:07 PDT)
- [AMBER] Generation of Topology and coordinate file for ionic liquid. Vidya Sundaram (Tue Jul 04 2017 - 22:22:04 PDT)
- Re: [AMBER] can't mutated Pro to Ala correctly during generating snapshots Daniel Roe (Wed Jul 05 2017 - 05:30:34 PDT)
- Re: [AMBER] AMber trajectory to Gromacs trajectory Daniel Roe (Wed Jul 05 2017 - 05:54:14 PDT)
- [AMBER] aMD Hamiltonian replica exchange Qinghua Liao (Wed Jul 05 2017 - 06:06:16 PDT)
- [AMBER] Amber Installation Rana Rehan Khalid (Wed Jul 05 2017 - 22:09:43 PDT)
- [AMBER] MMPBSA Delta total results NADIA RAHMAH (Thu Jul 06 2017 - 00:15:40 PDT)
- [AMBER] Using AMBER FF in NAMD to study Steered Molecular Dynamics (SMD) Bharat Manna (Thu Jul 06 2017 - 03:00:40 PDT)
- [AMBER] pytraj multihedral attributes Robert Wohlhueter (Thu Jul 06 2017 - 08:00:45 PDT)
- [AMBER] CPPTRAJ question: How to do RMS on a trajectory fragment? Jose Borreguero (Thu Jul 06 2017 - 11:41:58 PDT)
- [AMBER] non-realistic energies in MMPBSA giulia palermo (Thu Jul 06 2017 - 11:45:31 PDT)
- [AMBER] mismatch NTYPES for mixtures of 2 molecules Quynh Vo (Thu Jul 06 2017 - 16:28:30 PDT)
- [AMBER] Free energy calculation of Metalloprotein Garima Singh (Fri Jul 07 2017 - 04:02:29 PDT)
- Re: [AMBER] AMBER Digest, Vol 1985, Issue 1 Garima Singh (Fri Jul 07 2017 - 04:23:24 PDT)
- [AMBER] RESP charge fitting error in MCPB.py V3.0 abdennour braka (Fri Jul 07 2017 - 07:34:08 PDT)
- [AMBER] GPUs job and GUI issue Hirdesh Kumar (Fri Jul 07 2017 - 10:28:49 PDT)
- [AMBER] HIE CONVERT INTO HID Rana Rehan Khalid (Fri Jul 07 2017 - 12:44:11 PDT)
- [AMBER] MMPBSA.py.MPI errors with prmtop files on PBS platform Guqin Shi (Fri Jul 07 2017 - 15:47:10 PDT)
- [AMBER] Suggestions about Center and Image for multiple-molecule complex Guqin Shi (Sat Jul 08 2017 - 15:58:53 PDT)
- [AMBER] problem with cpptraj saving the average structure Ramin Salimi (Mon Jul 10 2017 - 03:07:21 PDT)
- [AMBER] tleap atom type and hybridization Lizelle Lubbe (Mon Jul 10 2017 - 05:04:06 PDT)
- [AMBER] charm-gui pdb incompatible with xleap Robert Wohlhueter (Mon Jul 10 2017 - 09:51:21 PDT)
- [AMBER] xleap fonts Robert Wohlhueter (Mon Jul 10 2017 - 11:51:14 PDT)
- [AMBER] About steered MD with pmemd and NMR restraints Yao Xiao (Mon Jul 10 2017 - 14:32:50 PDT)
- [AMBER] gamess installation Rana Rehan Khalid (Mon Jul 10 2017 - 19:19:41 PDT)
- [AMBER] parmed validity off-diagonal LJ parameters Lizelle Lubbe (Tue Jul 11 2017 - 08:00:59 PDT)
- [AMBER] error Rana Rehan Khalid (Tue Jul 11 2017 - 09:22:55 PDT)
- [AMBER] addAtomType Rana Rehan Khalid (Tue Jul 11 2017 - 19:20:32 PDT)
- [AMBER] How to perform analysis using ptraj Mustafa Alhaji Isa (Tue Jul 11 2017 - 23:01:53 PDT)
- [AMBER] A good multi GPU work-station James Starlight (Wed Jul 12 2017 - 01:46:40 PDT)
- [AMBER] micelle simulation Meng Wu (Wed Jul 12 2017 - 05:26:01 PDT)
- [AMBER] no output files of umbrella_file in ABMD Qinghua Liao (Wed Jul 12 2017 - 05:37:29 PDT)
- [AMBER] SDF (Spatial Distribution Function) calculation Saikat Pal (Wed Jul 12 2017 - 06:06:00 PDT)
- [AMBER] Sander MPI running over multiple nodes. Robinson, Roger (Wed Jul 12 2017 - 06:45:44 PDT)
- [AMBER] Amber installation Saikat Pal (Wed Jul 12 2017 - 08:01:30 PDT)
- [AMBER] cudaGetDeviceCount failed unknown error AMBER16 Hector Velazquez (Wed Jul 12 2017 - 12:16:18 PDT)
- [AMBER] A DNA-based short-term memory for biological deep learning Bill Ross (Wed Jul 12 2017 - 14:46:54 PDT)
- [AMBER] Problem with running mdout_analyzer.py Krantzman, Kristin D (Wed Jul 12 2017 - 15:40:42 PDT)
- [AMBER] MCPB.py issue Aldo Segura Cabrera (Wed Jul 12 2017 - 19:47:45 PDT)
- [AMBER] antechamber problem Michael Shokhen (Thu Jul 13 2017 - 02:15:28 PDT)
- [AMBER] prepin file for CMP ligand ARMIN HODAEI (Thu Jul 13 2017 - 04:40:29 PDT)
- [AMBER] cpptraj hbond Martina Devi (Thu Jul 13 2017 - 09:12:16 PDT)
- [AMBER] ERROR: The unperturbed charge of the unit: is not integral Li, Wen (Thu Jul 13 2017 - 11:38:01 PDT)
- [AMBER] cphstats Error: Could not open or parse cpin file Vincent Ustach (Thu Jul 13 2017 - 12:12:59 PDT)
- Re: [AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time SHAILESH KUMAR (Thu Jul 13 2017 - 14:01:47 PDT)
- [AMBER] PCA - first mode of motion Thakur, Abhishek (Thu Jul 13 2017 - 14:46:25 PDT)
- [AMBER] PMEMD module for Umbrella sampling Supriyo Naskar (Thu Jul 13 2017 - 21:45:42 PDT)
- [AMBER] parmchk2 closing loop error CA gmail (Fri Jul 14 2017 - 02:08:43 PDT)
- [AMBER] Umbrella sampling and weighted histogram analysis for binding energy calculation Investigador Química (Fri Jul 14 2017 - 11:40:04 PDT)
- [AMBER] micelle simulation problem Meng Wu (Sat Jul 15 2017 - 01:03:46 PDT)
- [AMBER] gcc error while compiling Amber16 on ubuntu16.04 Vivek Bharadwaj (Sat Jul 15 2017 - 14:17:17 PDT)
- [AMBER] FW: hbond analysis with CPPTRAJ Al Muhit, Baig Abdullah (Sat Jul 15 2017 - 17:05:43 PDT)
- [AMBER] hbond analysis with CPPTRAJ Al Muhit, Baig Abdullah (Sat Jul 15 2017 - 23:59:01 PDT)
- [AMBER] problem in CUDA-enabled Amber11 Pooja Kesari (Sun Jul 16 2017 - 06:35:36 PDT)
- [AMBER] Set-up the GPU cluster for AMBER James Starlight (Sun Jul 16 2017 - 06:49:25 PDT)
- [AMBER] hbond analysis with CPPTRAJ Baig abdullah Al muhit (Sun Jul 16 2017 - 08:19:19 PDT)
- [AMBER] Simulation of the mechanical stress in Amber James Starlight (Mon Jul 17 2017 - 00:53:32 PDT)
- [AMBER] pmemd.cuda vs pmemd.cuda.MPI Saikat Pal (Mon Jul 17 2017 - 05:03:21 PDT)
- [AMBER] Error in LEaP Dey, S. (Mon Jul 17 2017 - 08:55:10 PDT)
- [AMBER] NVIDIA quadro 5000 with Intel Xeon server for Amber-16 James Starlight (Mon Jul 17 2017 - 09:01:07 PDT)
- [AMBER] G09 Error Rana Rehan Khalid (Mon Jul 17 2017 - 11:38:12 PDT)
- [AMBER] MCPB.py tutorial - numbering issues Szymon Żaczek (Mon Jul 17 2017 - 11:54:33 PDT)
- Re: [AMBER] AMBER Digest, Vol 1994, Issue 1 Hector Velazquez (Mon Jul 17 2017 - 12:44:21 PDT)
- [AMBER] Log file for Reweighting Parthiban Marimuthu (Mon Jul 17 2017 - 14:58:50 PDT)
- [AMBER] CPPTRAJ analysis on PDB trajectory with TIP4P water from GROMACS Ming Tang (Mon Jul 17 2017 - 19:08:13 PDT)
- [AMBER] Chi plot tryptophan. Saman Yousuf ali (Mon Jul 17 2017 - 22:07:16 PDT)
- [AMBER] amber12 cpptraj runanalysis Martina Devi (Tue Jul 18 2017 - 07:21:29 PDT)
- [AMBER] parmed/intermol gromacs to amber Neha Gandhi (Tue Jul 18 2017 - 17:56:38 PDT)
- [AMBER] Error come after executing this command MCPB.py -i 4ZF6.in -s 2 Rana Rehan Khalid (Tue Jul 18 2017 - 20:38:51 PDT)
- [AMBER] problem Finding entropy Ramin Salimi (Tue Jul 18 2017 - 21:33:47 PDT)
- [AMBER] How do I perform LIE analysis for a metalloprotein containing Cd using Amber ? Garima Singh (Wed Jul 19 2017 - 02:50:39 PDT)
- [AMBER] amb2gmx.pl script not working Dey, S. (Wed Jul 19 2017 - 05:27:17 PDT)
- [AMBER] QM/MM Minimization with restraints Sonia Romero (Wed Jul 19 2017 - 06:07:45 PDT)
- [AMBER] vlimit error sangita kachhap (Wed Jul 19 2017 - 07:54:01 PDT)
- [AMBER] Orca interface for QM/MM James Kress (Wed Jul 19 2017 - 10:03:28 PDT)
- [AMBER] Log file for Reweighting Parthiban Marimuthu (Wed Jul 19 2017 - 12:48:12 PDT)
- [AMBER] Use energy fluctuations as the criterion of equilibrium in the NPT ensembles? Xing (Wed Jul 19 2017 - 17:02:33 PDT)
- [AMBER] ion distribution-doubt Mary Varughese (Wed Jul 19 2017 - 23:38:29 PDT)
- [AMBER] Simulation of the mechanical stress James Starlight (Thu Jul 20 2017 - 02:14:23 PDT)
- [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Alonso Martinez, Diego (Thu Jul 20 2017 - 06:05:39 PDT)
- Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Adrian Roitberg (Thu Jul 20 2017 - 06:22:36 PDT)
- Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Carlos Simmerling (Thu Jul 20 2017 - 06:40:57 PDT)
- Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Alonso Martinez, Diego (Thu Jul 20 2017 - 11:58:46 PDT)
- Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Adrian Roitberg (Thu Jul 20 2017 - 12:04:35 PDT)
- Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Alonso Martinez, Diego (Thu Jul 20 2017 - 12:19:39 PDT)
- Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Adrian Roitberg (Thu Jul 20 2017 - 12:23:34 PDT)
- Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Bill Ross (Thu Jul 20 2017 - 12:23:55 PDT)
- Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Alonso Martinez, Diego (Thu Jul 20 2017 - 12:33:00 PDT)
- Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Hai Nguyen (Thu Jul 20 2017 - 12:38:41 PDT)
- Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Bill Ross (Thu Jul 20 2017 - 13:00:24 PDT)
- [AMBER] Buying-renting GPU/CPU time for amber MD simulations George Tzotzos (Thu Jul 20 2017 - 08:38:16 PDT)
- [AMBER] Functions in NAB Akshar Sharma (Thu Jul 20 2017 - 08:54:23 PDT)
- [AMBER] His getting protonated to HIP Thakur, Abhishek (Thu Jul 20 2017 - 15:26:50 PDT)
- [AMBER] Problems in using GLYCAM force field Meng Wu (Fri Jul 21 2017 - 05:17:32 PDT)
- [AMBER] Distance restraint during production md Lizelle Lubbe (Sat Jul 22 2017 - 10:51:43 PDT)
- [AMBER] INSTALLING AMBER IN WINDOWS K. Subashini (Sun Jul 23 2017 - 01:08:49 PDT)
- [AMBER] Use of DFTB3 with Dispersion Correction Christian Wiebeler (Sun Jul 23 2017 - 10:36:21 PDT)
- [AMBER] Extracting trajectory without the periodic boundary conditions usng ptraj Shilpa Gupta (Sun Jul 23 2017 - 10:55:18 PDT)
- [AMBER] Mcpbpy empirical method Lizelle Lubbe (Mon Jul 24 2017 - 04:32:19 PDT)
- [AMBER] SASA calculation using LCPO method Garima Singh (Mon Jul 24 2017 - 04:34:58 PDT)
- [AMBER] gpu %utils vs mem used Meij, Henk (Mon Jul 24 2017 - 11:20:39 PDT)
- [AMBER] Is it possible to align frames? Elisa Pieri (Mon Jul 24 2017 - 12:59:17 PDT)
- [AMBER] ncsu_smd codes with pmemd in Amber 16 Yao Xiao (Mon Jul 24 2017 - 13:58:51 PDT)
- [AMBER] Grid visualization for ions- doubt maryvj1985 (Mon Jul 24 2017 - 22:54:05 PDT)
- [AMBER] Free Energy, mutating an amino acid Johannes Loeffler (Mon Jul 24 2017 - 23:09:11 PDT)
- [AMBER] MPI Error in Amber Installation Debasish Mandal (Tue Jul 25 2017 - 02:10:05 PDT)
- [AMBER] wheel representation of torsional angle Saikat Pal (Tue Jul 25 2017 - 06:28:47 PDT)
- [AMBER] Mcpb.py prepared .com input small file MCPB.py -i 4ZF6.in -s 1 Rana Rehan Khalid (Tue Jul 25 2017 - 15:30:26 PDT)
- [AMBER] Query regarding 3D-RISM Rakesh Srivastava (Tue Jul 25 2017 - 22:55:57 PDT)
- [AMBER] counting ions - doubt-urgent Mary Varughese (Wed Jul 26 2017 - 03:05:15 PDT)
- [AMBER] Difference between AMBER 14 pmemd.cuda and AMBER 12 pmemd.cuda Saikat Pal (Wed Jul 26 2017 - 07:34:36 PDT)
- [AMBER] Mutating DNA bases Debostuti Ghoshdastidar (Thu Jul 27 2017 - 05:12:08 PDT)
- [AMBER] Manual parameterization of the TIP4P/2005 water model Hannes Konegger (Thu Jul 27 2017 - 07:13:41 PDT)
- [AMBER] adaptive biasing force (ABF) method in AMBER? Xing (Thu Jul 27 2017 - 10:44:52 PDT)
- [AMBER] How to make a phenol monolayer Ramin Salimi (Thu Jul 27 2017 - 14:36:55 PDT)
- [AMBER] gaff Milo Westler (Thu Jul 27 2017 - 16:17:16 PDT)
- [AMBER] PBC problem with autoimage&image Meng Wu (Thu Jul 27 2017 - 21:37:06 PDT)
- [AMBER] question about the error when I start up the xleap 方煜 (Thu Jul 27 2017 - 21:42:14 PDT)
- [AMBER] Error analyzing temperature Núbia Prates (Fri Jul 28 2017 - 08:16:13 PDT)
- [AMBER] Atoms do not have type Error for G-quadruplex DNA. Jerrano Bowleg (Sun Jul 30 2017 - 09:12:07 PDT)
- [AMBER] "Length of coordinates and ESP charges are different" in MCPB.py -s3 Eugene Cha (Mon Jul 31 2017 - 03:59:56 PDT)
- [AMBER] How to use cpptraj in AMBER10 to generate RMSD and RMSF Mustafa Alhaji Isa (Mon Jul 31 2017 - 07:35:19 PDT)
- Last message date: Mon Jul 31 2017 - 15:00:02 PDT
- Archived on: Fri Nov 15 2024 - 05:55:36 PST
