Amber Archive Jul 2019 by thread
- [AMBER] RESP charge calculation Sadaf Rani (Mon Jul 01 2019 - 03:39:39 PDT)
- [AMBER] Thermodynamic information of RISM Eugene huh (Mon Jul 01 2019 - 04:12:20 PDT)
- [AMBER] AMBER G09 RESP Calculation problem Gustaf Olsson (Mon Jul 01 2019 - 04:22:54 PDT)
- Re: [AMBER] Regarding nmode error David A Case (Mon Jul 01 2019 - 05:57:14 PDT)
- [AMBER] Antechamber Charge Methods Sofia Vasilakaki (Mon Jul 01 2019 - 07:26:10 PDT)
- Re: [AMBER] Error: "System must be very inhomogeneous" Lucas Bandeira (Mon Jul 01 2019 - 09:33:42 PDT)
- Re: [AMBER] changes in periodic box dimensions after pmemd.cuda run Violeta Burns Casamayor (Mon Jul 01 2019 - 10:12:29 PDT)
- [AMBER] REMD error Marcela Madrid (Mon Jul 01 2019 - 17:13:24 PDT)
- Re: [AMBER] MD Simulation in DMSO Rodriguez, Yoel (Tue Jul 02 2019 - 01:14:18 PDT)
- [AMBER] R . E. D Kolattukudy P. Santo (Tue Jul 02 2019 - 06:47:00 PDT)
- [AMBER] Amberff14sb Dylan Tasse (Tue Jul 02 2019 - 07:52:07 PDT)
- [AMBER] memtestG80 alternative ? - testing actual GPUs regarding soft errors Marek Maly (Tue Jul 02 2019 - 08:37:55 PDT)
- Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE Sadaf Rani (Tue Jul 02 2019 - 11:23:31 PDT)
- [AMBER] unwrap in pytraj? Shayna Hilburg (Tue Jul 02 2019 - 13:49:59 PDT)
- [AMBER] problem about print_res 谭畅 (Tue Jul 02 2019 - 18:15:52 PDT)
- [AMBER] SIGSEVV error on test_at_serial for QMMM interface and miniconda installation problem thrugh amberTools Francesca Lønstad Bleken (Wed Jul 03 2019 - 01:28:11 PDT)
- [AMBER] install Amber16 Bacaita Simona (Wed Jul 03 2019 - 04:47:53 PDT)
- Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat James Starlight (Wed Jul 03 2019 - 06:10:47 PDT)
- [AMBER] on the choosing of the cut-off value for PME with Amber14SB James Starlight (Wed Jul 03 2019 - 06:16:52 PDT)
- [AMBER] Error in prmtop and inpcrd atom shivangi agarwal (Wed Jul 03 2019 - 10:06:19 PDT)
- [AMBER] Fwd: Fwd: please clarify this answer Charu Sharma (JRF) (Wed Jul 03 2019 - 10:22:52 PDT)
- [AMBER] Glycan naming problem Rui Chen (Wed Jul 03 2019 - 21:28:32 PDT)
- Re: [AMBER] SIGSEVV error on test_at_serial for QMMM Francesca Lønstad Bleken (Wed Jul 03 2019 - 22:42:38 PDT)
- [AMBER] How to print the total Potential Energy for an atom? Biplab Ghosh (Thu Jul 04 2019 - 02:09:05 PDT)
- [AMBER] How to replicate the number of lipids in bilayer for membrane dynamics Maria Bzówka (Fri Jul 05 2019 - 01:46:01 PDT)
- [AMBER] parmchk2 and acceptable penalty score Prasanth G, Research Scholar (Fri Jul 05 2019 - 10:08:49 PDT)
- [AMBER] MCPB.py generated parameters in leap SARAH JEANNE LEFAVE (Fri Jul 05 2019 - 10:13:18 PDT)
- [AMBER] Fwd: amber installation problem Charu Sharma (JRF) (Sat Jul 06 2019 - 00:26:21 PDT)
- [AMBER] Fwd: Charu Sharma (JRF) (Sat Jul 06 2019 - 04:20:57 PDT)
- [AMBER] GROMACS to AMBER .top and .pdb conversion using gromber cpimenta (Sat Jul 06 2019 - 04:56:44 PDT)
- [AMBER] Adding external forces to amber Mohammad Hassan Khatami (Sat Jul 06 2019 - 06:59:49 PDT)
- Re: [AMBER] Perturbing residue co-ordinates within a solvated truncated octohedral box David Case (Sun Jul 07 2019 - 04:34:41 PDT)
- [AMBER] RESP charges Sadaf Rani (Sun Jul 07 2019 - 11:45:38 PDT)
- [AMBER] closest distance between ligand and particular amino-acid residues during MD simulation Rinsha Chk (Mon Jul 08 2019 - 04:28:44 PDT)
- [AMBER] EPW "ATOMS Moving too fast" - TIP4PEW Bowman, Jacob (Mon Jul 08 2019 - 10:25:03 PDT)
- [AMBER] Export command not found (export CUDA_VISIBLE_DEVICES) Amen Shamim (Mon Jul 08 2019 - 11:05:54 PDT)
- [AMBER] Fwd: Charu Sharma (JRF) (Tue Jul 09 2019 - 01:08:47 PDT)
- [AMBER] Constant pH MD + HMR Nikolay N. Kuzmich (Tue Jul 09 2019 - 04:43:25 PDT)
- [AMBER] Fwd: Charu Sharma (JRF) (Tue Jul 09 2019 - 06:43:31 PDT)
- [AMBER] mpirun <defunct> with pmemd.cuda.MPI on EXXACT systems Jardin, Christophe Dr. (Tue Jul 09 2019 - 06:57:48 PDT)
- [AMBER] amber14sb.ff Dylan Tasse (Tue Jul 09 2019 - 07:41:45 PDT)
- [AMBER] There is a bond of 8.882728 angstroms between: [Blank] Anthony Bogetti (Tue Jul 09 2019 - 08:40:58 PDT)
- [AMBER] electrostatic energy of mmgbsa decomposition 谭畅 (Wed Jul 10 2019 - 00:49:48 PDT)
- Re: [AMBER] set RA, RT and n_partition in adQM/MM run Ruth Helena Tichauer (Wed Jul 10 2019 - 03:41:39 PDT)
- [AMBER] Compiling MPI 3D-RISM Rakesh Srivastava (Wed Jul 10 2019 - 03:50:07 PDT)
- [AMBER] To stop the message service Vishnudatt Pandey (Wed Jul 10 2019 - 03:57:29 PDT)
- [AMBER] About -dr option in Antechamber Alan (Wed Jul 10 2019 - 04:53:19 PDT)
- [AMBER] How to generate topology file for protein-ATP complex 李耀 (Wed Jul 10 2019 - 07:51:54 PDT)
- [AMBER] Significant deviation in electrostatics, (EEL/EGL values) Aswin Hanagal (Wed Jul 10 2019 - 08:11:56 PDT)
- [AMBER] salt concentration in the production run and MMPBSA Prasanth G, Research Scholar (Wed Jul 10 2019 - 09:50:55 PDT)
- [AMBER] conformational sampling for organic/drug-like compounds Vaibhav Dixit (Wed Jul 10 2019 - 11:16:12 PDT)
- [AMBER] Cluster Analysis with CPPTRAJ Lod King (Wed Jul 10 2019 - 19:39:45 PDT)
- Re: [AMBER] Issue installing Amber18 pbsa.cuda Ruxi Qi (Wed Jul 10 2019 - 20:34:08 PDT)
- [AMBER] Query regarding 3D-RISM thermodynamic output format Leena Aggarwal (Wed Jul 10 2019 - 23:46:08 PDT)
- [AMBER] vlimit exceeded and volume of ucell too big, too many subcells during adQM/MM dynamics Ruth Helena Tichauer (Thu Jul 11 2019 - 00:36:30 PDT)
- [AMBER] PM6 charges for MD with AMBER Thomas Evangelidis (Thu Jul 11 2019 - 02:52:34 PDT)
- [AMBER] Error in saving prmtop and inpcrd shivangi agarwal (Fri Jul 12 2019 - 01:42:24 PDT)
- [AMBER] Problem with Phenylphosphonic acid Gustaf Olsson (Fri Jul 12 2019 - 06:15:34 PDT)
- [AMBER] CUDA errors on a 700k system Dmitry Suplatov (Sun Jul 14 2019 - 11:00:51 PDT)
- [AMBER] Force field for Cecl3, Lacl3 and Prcl3 Satyaseelan C (Mon Jul 15 2019 - 02:04:16 PDT)
- [AMBER] How to change the coordinates of the system Maria Bzówka (Mon Jul 15 2019 - 04:32:32 PDT)
- [AMBER] close contact between atoms Sadaf Rani (Mon Jul 15 2019 - 13:22:05 PDT)
- [AMBER] Error in MMPBSA calculation Shilpa Gupta (Tue Jul 16 2019 - 00:03:02 PDT)
- [AMBER] Recent Force Fields for nucleotides Alessandro LANDI (Tue Jul 16 2019 - 04:11:14 PDT)
- [AMBER] Umbrella Sampling: frequency restraint emanuele falbo (Wed Jul 17 2019 - 02:21:35 PDT)
- [AMBER] Print out velocities from a restart-crd file Felipe Franco (Wed Jul 17 2019 - 04:36:15 PDT)
- [AMBER] Problem with barostat during the production stage (membrane simulation) Maria Bzówka (Wed Jul 17 2019 - 06:10:52 PDT)
- [AMBER] Covariance Matrix of residues center of mass Guadalupe Alvarez (Wed Jul 17 2019 - 07:42:01 PDT)
- [AMBER] Adding Na+ Anuja Ware (Wed Jul 17 2019 - 08:21:03 PDT)
- [AMBER] How to prepare correct gaussian input for RESP charge calculation? Sadaf Rani (Wed Jul 17 2019 - 12:03:34 PDT)
- [AMBER] Error with make test after installing Amber14 and AmberTools15 A K (Wed Jul 17 2019 - 17:30:05 PDT)
- [AMBER] Posits preparing to pounce on Floating Point Bill Ross (Wed Jul 17 2019 - 20:29:52 PDT)
- [AMBER] pca - Projecting vectors onto a trajectory Prasanth G, Research Scholar (Thu Jul 18 2019 - 03:40:34 PDT)
- [AMBER] Help with parameters for iron centers Sérgio Marques (Thu Jul 18 2019 - 05:00:39 PDT)
- [AMBER] error in mmpbsa Fransiska Kurniawan (Fri Jul 19 2019 - 02:24:16 PDT)
- [AMBER] Error: "Bad data for namelist object statene" with constant pH RE simulation Jardin, Christophe Dr. (Fri Jul 19 2019 - 04:30:12 PDT)
- [AMBER] Energy different between igb=0 and igb=6 during vacuum minimization with sander Jingxiao Bao (Fri Jul 19 2019 - 06:52:44 PDT)
- Re: [AMBER] New ACPYPE server Matias Machado (Fri Jul 19 2019 - 11:30:51 PDT)
- [AMBER] Parameter file for GTP or GMP containing tRNA student_cbc_1 nnlab (Sun Jul 21 2019 - 08:38:11 PDT)
- [AMBER] hbond 谭畅 (Mon Jul 22 2019 - 08:45:37 PDT)
- [AMBER] Ligand-Resp-Gaussian Prasanth G, Research Scholar (Mon Jul 22 2019 - 09:26:31 PDT)
- [AMBER] Error in preparing system using AmberTools19 shivangi agarwal (Mon Jul 22 2019 - 09:29:44 PDT)
- [AMBER] Error in resp charge calculation Sadaf Rani (Mon Jul 22 2019 - 13:20:46 PDT)
- [AMBER] Calculating area per lipid for system with different numbers of lipids on leaflets Maria Bzówka (Tue Jul 23 2019 - 02:24:03 PDT)
- [AMBER] Large increase in polarization energy during MD CROUZY Serge 119222 (Tue Jul 23 2019 - 04:39:59 PDT)
- [AMBER] Problems with RTX2080Ti Giovanni Grazioso (Tue Jul 23 2019 - 05:55:58 PDT)
- [AMBER] Can't load trajectory in coordinate formate from amber in VMD Xikun Liu (Tue Jul 23 2019 - 18:35:46 PDT)
- [AMBER] Combing trajectoty mwli.mail.ustc.edu.cn (Tue Jul 23 2019 - 18:46:18 PDT)
- [AMBER] Reference for External electric field implementation in Amber Kshatresh Dutta Dubey (Tue Jul 23 2019 - 21:15:00 PDT)
- [AMBER] -regarding failure in addition of Na+ ions in tleap Patil Pranita Uttamrao (Wed Jul 24 2019 - 07:26:22 PDT)
- [AMBER] problem with building cpptraj in AmberTools19 David Case (Wed Jul 24 2019 - 10:17:52 PDT)
- [AMBER] Query on linear interaction energy (lie) calculation using CPPTRAJ Bharat Manna (Wed Jul 24 2019 - 21:49:16 PDT)
- [AMBER] reg: residue number order like pdb Lara rajam (Thu Jul 25 2019 - 11:23:07 PDT)
- [AMBER] Amber installation problem Debasish Mandal (Fri Jul 26 2019 - 03:03:25 PDT)
- [AMBER] MMPBSA for Absolute free energy Lod King (Fri Jul 26 2019 - 12:00:50 PDT)
- [AMBER] Switch function in NAMDEnergy cooresponds to AMBER input flag Lod King (Fri Jul 26 2019 - 13:38:50 PDT)
- [AMBER] Kinetic Energy is zero in production run. Amit Kumar (Sat Jul 27 2019 - 04:38:18 PDT)
- [AMBER] General questions regarding MMPBSA in AMBER Lod King (Sat Jul 27 2019 - 10:19:25 PDT)
- [AMBER] Using pmemd.gem (Amoeba) with nmropt=1 Luboš Plamitzer (Sat Jul 27 2019 - 12:33:16 PDT)
- [AMBER] Regarding cut-off distance in hydrogen bond richa anand (Sun Jul 28 2019 - 07:32:03 PDT)
- [AMBER] Swarms-of-trajectories example files Federico Olivieri (Sun Jul 28 2019 - 18:34:12 PDT)
- [AMBER] TI for mutation of charged residues Hosein Geraili Daronkola (Mon Jul 29 2019 - 00:17:05 PDT)
- [AMBER] missing bond parameter for Mg ion Chen, Wei (Mon Jul 29 2019 - 14:35:22 PDT)
- [AMBER] pbsa calculation Lod King (Mon Jul 29 2019 - 17:38:24 PDT)
- [AMBER] modelling of a penta coordination around zinc ion (+2) using MCPB.py SATYAJIT KHATUA (Mon Jul 29 2019 - 22:22:50 PDT)
- [AMBER] question about GIST calculation Aliakbartehrani Zahra (Tue Jul 30 2019 - 03:17:04 PDT)
- [AMBER] Non-standard Hydrogen Bonding Loris Moretti (Tue Jul 30 2019 - 05:25:46 PDT)
- [AMBER] Simulating Water-Metal Interface with NPT Ensemble Lucas Bandeira (Tue Jul 30 2019 - 12:31:32 PDT)
- [AMBER] MCPB.py showing error in the step: MCPB.py -i 1OKL.in -s 2 Divya Rai (Wed Jul 31 2019 - 05:09:24 PDT)
- [AMBER] Problem running Antechamber for GTP Akinpelu Olayinka (Wed Jul 31 2019 - 11:12:37 PDT)
- Last message date: Wed Jul 31 2019 - 13:30:03 PDT
- Archived on: Fri Nov 15 2024 - 05:55:54 PST
