Amber Archive Jul 2015: by subject

[AMBER] "nstlim" is not reflected correctly in REMD with pmemd.MPI
- Gerald Monard (Tue Jul 21 2015 - 06:46:20 PDT)
- kurisaki (Tue Jul 21 2015 - 05:33:55 PDT)
- kurisaki (Tue Jul 21 2015 - 04:16:30 PDT)
[AMBER] [cpptraj] Nativecontacts failing with long trajectory
- Juan Eiros Zamora (Fri Jul 24 2015 - 03:21:30 PDT)
- Daniel Roe (Thu Jul 23 2015 - 08:48:54 PDT)
- Juan Eiros Zamora (Thu Jul 23 2015 - 00:59:57 PDT)
- Daniel Roe (Wed Jul 22 2015 - 13:53:18 PDT)
- Juan Eiros Zamora (Wed Jul 22 2015 - 12:36:08 PDT)
[AMBER] About charge derivation for enantiomeric molecules
- Casalini Tommaso (Sat Jul 11 2015 - 05:48:49 PDT)
- case (Sat Jul 11 2015 - 05:41:25 PDT)
- Tommaso Casalini (Sat Jul 11 2015 - 02:30:39 PDT)
[AMBER] About charge derivation for enantiomers
- Tommaso Casalini (Fri Jul 10 2015 - 13:51:40 PDT)
[AMBER] About python usage in AmberTools
- Jason Swails (Wed Jul 08 2015 - 12:07:06 PDT)
- Hai Nguyen (Wed Jul 08 2015 - 09:42:10 PDT)
- Hai Nguyen (Wed Jul 08 2015 - 09:37:20 PDT)
- Juan Eiros Zamora (Wed Jul 08 2015 - 07:26:35 PDT)
- Jason Swails (Wed Jul 08 2015 - 07:20:13 PDT)
- Juan Eiros Zamora (Wed Jul 08 2015 - 07:19:02 PDT)
- Jason Swails (Wed Jul 08 2015 - 06:59:11 PDT)
- Juan Eiros Zamora (Wed Jul 08 2015 - 06:31:46 PDT)
- Hai Nguyen (Tue Jul 07 2015 - 14:54:30 PDT)
- Jason Swails (Tue Jul 07 2015 - 12:54:19 PDT)
- Eiros Zamora, Juan (Tue Jul 07 2015 - 12:50:45 PDT)
- Jason Swails (Tue Jul 07 2015 - 11:55:28 PDT)
- Hai Nguyen (Tue Jul 07 2015 - 11:33:42 PDT)
- Juan Eiros Zamora (Tue Jul 07 2015 - 11:05:23 PDT)
[AMBER] Accelerated md for protein dna complex with modified residue
- Vlad Cojocaru (Wed Jul 15 2015 - 06:11:13 PDT)
- Muthukumaran R (Tue Jul 14 2015 - 11:05:59 PDT)
[AMBER] AMBER Digest, Vol 1274, Issue 1
- Hai Nguyen (Thu Jul 09 2015 - 15:33:46 PDT)
- Eleftherios A P Lambros (Thu Jul 09 2015 - 15:12:58 PDT)
- Eleftherios A P Lambros (Thu Jul 09 2015 - 14:16:36 PDT)
[AMBER] AMBER error : Coordinate resetting (SHAKE) cannot be accomplish ed
- David A Case (Thu Jul 16 2015 - 05:42:02 PDT)
- MASAOKI FUJII (Thu Jul 16 2015 - 00:37:37 PDT)
[AMBER] Amber for phophorylated residue
- Ziba Bahadori (Thu Jul 23 2015 - 08:27:39 PDT)
- David A Case (Thu Jul 23 2015 - 07:45:29 PDT)
- Ziba Bahadori (Thu Jul 23 2015 - 03:12:19 PDT)
[AMBER] amber topology file for cytochrome c covalently bond to Heme
- David A Case (Tue Jul 07 2015 - 10:27:42 PDT)
- Shoresh Shafei (Mon Jul 06 2015 - 10:07:58 PDT)
[AMBER] Ambertools15 installation without Amber
- Gerald Monard (Thu Jul 02 2015 - 04:49:46 PDT)
- ANWESHA SARKAR (Thu Jul 02 2015 - 03:25:37 PDT)
- Gerald Monard (Thu Jul 02 2015 - 02:54:32 PDT)
- ANWESHA SARKAR (Thu Jul 02 2015 - 02:45:47 PDT)
- Gerald Monard (Thu Jul 02 2015 - 02:30:12 PDT)
- ANWESHA SARKAR (Thu Jul 02 2015 - 02:16:42 PDT)
[AMBER] anisotropic vs. semi-isotropic membrane simulations
- David A Case (Thu Jul 02 2015 - 06:19:27 PDT)
- Jason Swails (Thu Jul 02 2015 - 05:34:25 PDT)
- Ross Walker (Wed Jul 01 2015 - 15:48:05 PDT)
- Naomi Rose Latorraca (Wed Jul 01 2015 - 15:01:51 PDT)
[AMBER] another leap inconsistency
- hannes.loeffler.stfc.ac.uk (Fri Jul 03 2015 - 13:02:49 PDT)
- Jason Swails (Thu Jul 02 2015 - 07:53:31 PDT)
- Hannes Loeffler (Thu Jul 02 2015 - 06:44:03 PDT)
[AMBER] Antechamber for boronic acid derivatives?
- Michael Shokhen (Thu Jul 30 2015 - 00:19:17 PDT)
[AMBER] articles published for ff14SB and GBneck2
- Vlad Cojocaru (Fri Jul 10 2015 - 05:45:35 PDT)
- Carlos Simmerling (Thu Jul 09 2015 - 07:03:56 PDT)
[AMBER] assigning atom type and charge
- FyD (Thu Jul 09 2015 - 01:51:58 PDT)
- Jason Swails (Mon Jul 06 2015 - 05:50:32 PDT)
- Sanjib Paul (Mon Jul 06 2015 - 04:41:08 PDT)
[AMBER] atom mapping
- Daniel Roe (Sun Jul 12 2015 - 08:30:33 PDT)
- Gard Nelson (Fri Jul 10 2015 - 11:38:40 PDT)
[AMBER] Changing NMR restraint weights
- David A Case (Tue Jul 14 2015 - 08:48:29 PDT)
- Oliver Grant (Tue Jul 14 2015 - 07:02:35 PDT)
- David A Case (Mon Jul 13 2015 - 06:52:04 PDT)
- Oliver Grant (Fri Jul 10 2015 - 02:02:29 PDT)
[AMBER] charmmlipid2amber.py
- Ramin Ekhteiari (Sat Jul 04 2015 - 11:35:49 PDT)
[AMBER] Chlorophyll A .mol2 file
- Ofir Tal (Thu Jul 02 2015 - 06:45:12 PDT)
[AMBER] Cluster restraints
- David A Case (Tue Jul 28 2015 - 17:49:47 PDT)
- Damiano Spadoni (Tue Jul 28 2015 - 09:24:39 PDT)
[AMBER] compare two trajectories
- Hai Nguyen (Fri Jul 10 2015 - 12:41:27 PDT)
- Xing (Fri Jul 10 2015 - 12:35:10 PDT)
[AMBER] Compile Failure
- David A Case (Thu Jul 02 2015 - 06:13:00 PDT)
- Jim Wu (Wed Jul 01 2015 - 09:38:56 PDT)
- David A Case (Wed Jul 01 2015 - 05:41:39 PDT)
[AMBER] Coordinate resetting (SHAKE) cannot be accomplished
- David A Case (Thu Jul 16 2015 - 05:36:58 PDT)
- Vahid Kshani (Wed Jul 15 2015 - 22:27:59 PDT)
[AMBER] countless warnning
- Ray Luo, Ph.D. (Fri Jul 17 2015 - 11:34:13 PDT)
- Albert (Fri Jul 17 2015 - 08:17:10 PDT)
[AMBER] CPPTRAJ - Filtering frames based on lowest of the two RMSD values
- Daniel Roe (Mon Jul 20 2015 - 16:40:53 PDT)
- Hai Nguyen (Mon Jul 20 2015 - 16:00:43 PDT)
- Stevens, David (Mon Jul 20 2015 - 15:30:00 PDT)
[AMBER] Cpptraj able to identify coordinates written by VMD?
- Thomas Cheatham (Thu Jul 02 2015 - 12:47:48 PDT)
- Brian Radak (Thu Jul 02 2015 - 11:58:19 PDT)
- Karl Debiec (Thu Jul 02 2015 - 10:31:48 PDT)
[AMBER] Cpptraj failure
- Lin Song (Mon Jul 13 2015 - 09:14:42 PDT)
- Daniel Roe (Thu Jul 02 2015 - 09:45:37 PDT)
[AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory
- Daniel Roe (Thu Jul 30 2015 - 08:19:43 PDT)
- bharat lakhani (Wed Jul 29 2015 - 19:47:32 PDT)
[AMBER] cpptraj: bounds command -> grid
- Daniel Roe (Tue Jul 07 2015 - 03:24:27 PDT)
- Thomas Fox (Tue Jul 07 2015 - 00:10:11 PDT)
[AMBER] cpptraj: rmsd problem
- Daniel Roe (Tue Jul 07 2015 - 07:20:17 PDT)
- Thomas Fox (Tue Jul 07 2015 - 02:15:34 PDT)
[AMBER] CpptrajPairDist
- Daniel Roe (Thu Jul 23 2015 - 08:56:55 PDT)
- bharat lakhani (Tue Jul 21 2015 - 19:50:08 PDT)
[AMBER] Deleting multiple atoms in xleap
- Jason Swails (Sat Jul 18 2015 - 07:29:36 PDT)
- jacob wick (Fri Jul 17 2015 - 05:58:35 PDT)
- jacob wick (Fri Jul 17 2015 - 05:32:54 PDT)
[AMBER] detecting and removing corrupted frames
- Daniel Roe (Mon Jul 27 2015 - 06:24:35 PDT)
- Thomas Evangelidis (Mon Jul 27 2015 - 03:32:23 PDT)
[AMBER] Distance restraint in AMBER 14 and GPU
- David A Case (Mon Jul 20 2015 - 07:28:28 PDT)
- Lionel Sacconnay (Mon Jul 20 2015 - 02:28:23 PDT)
[AMBER] Error in loading inpcrd file in sander
- Mohsen Zakeri (Tue Jul 21 2015 - 15:26:08 PDT)
- Daniel Roe (Tue Jul 21 2015 - 15:24:30 PDT)
- Mohsen Zakeri (Tue Jul 21 2015 - 15:08:49 PDT)
- Mohsen Zakeri (Tue Jul 21 2015 - 15:06:14 PDT)
- Daniel Roe (Tue Jul 21 2015 - 14:52:50 PDT)
- Hai Nguyen (Tue Jul 21 2015 - 14:41:15 PDT)
- Mohsen Zakeri (Tue Jul 21 2015 - 14:29:25 PDT)
[AMBER] Error in writing .lib file
- Elvis Martis (Fri Jul 17 2015 - 01:04:15 PDT)
- David A Case (Thu Jul 16 2015 - 05:30:21 PDT)
- Elvis Martis (Wed Jul 15 2015 - 20:13:18 PDT)
[AMBER] ESURF term in MMGBSA
- Jason Swails (Fri Jul 10 2015 - 04:58:20 PDT)
- Ahmed Ayoub (Thu Jul 09 2015 - 19:46:54 PDT)
[AMBER] ETOT drift and nscm in NVE for calculation of diffusion
- Jason Swails (Tue Jul 21 2015 - 15:36:12 PDT)
- CHAMI F. (Tue Jul 14 2015 - 11:13:52 PDT)
[AMBER] Explicit Solvent Constant pH MD
- Jason Swails (Sat Jul 11 2015 - 05:50:55 PDT)
- Rahul Ramesh (Fri Jul 10 2015 - 14:52:52 PDT)
- Alan (Thu Jul 09 2015 - 13:47:05 PDT)
- Jason Swails (Thu Jul 09 2015 - 09:49:38 PDT)
- Rahul Ramesh (Thu Jul 09 2015 - 09:42:17 PDT)
[AMBER] Explicit solvent pH-REMD
- Jason Swails (Wed Jul 22 2015 - 09:47:37 PDT)
- whb (Wed Jul 22 2015 - 07:33:14 PDT)
[AMBER] Explicit-solvent-pH-REMD
- Jason Swails (Fri Jul 31 2015 - 05:16:56 PDT)
- whb (Fri Jul 31 2015 - 00:48:28 PDT)
[AMBER] extract coordinates of a specific atom
- Nhai (Fri Jul 03 2015 - 16:50:42 PDT)
- Morteza Chehel Amirani (Fri Jul 03 2015 - 16:43:20 PDT)
[AMBER] FATAL: Atom () does not have a type????
- Kenneth Huang (Fri Jul 10 2015 - 15:16:38 PDT)
- Evans, Shalton (Fri Jul 10 2015 - 14:32:49 PDT)
- Kenneth Huang (Fri Jul 10 2015 - 13:55:47 PDT)
- Evans, Shalton (Fri Jul 10 2015 - 13:36:05 PDT)
[AMBER] FEW tutorial
- Hannes Loeffler (Fri Jul 10 2015 - 03:54:23 PDT)
- Mohsen Zakeri (Fri Jul 10 2015 - 03:37:43 PDT)
[AMBER] folding RNA using SGLD
- Asmita Gupta (Thu Jul 02 2015 - 05:49:02 PDT)
[AMBER] frames in mmpbsa.py
- Jason Swails (Mon Jul 20 2015 - 07:27:51 PDT)
- Albert (Sun Jul 19 2015 - 23:10:16 PDT)
- Jason Swails (Fri Jul 17 2015 - 12:51:23 PDT)
- Albert (Fri Jul 17 2015 - 03:12:45 PDT)
[AMBER] Fwd: NMR restraints with pmemd.cuda problem
- Miroslav Krepl (Thu Jul 30 2015 - 02:43:04 PDT)
[AMBER] Gaff Parameters Si
- Sharapa (Thu Jul 30 2015 - 04:30:51 PDT)
- David A Case (Tue Jul 21 2015 - 05:58:29 PDT)
- Sharapa (Mon Jul 20 2015 - 16:08:47 PDT)
[AMBER] GPU EVGA GTX 980 SC ACX
- Ross Walker (Sat Jul 25 2015 - 14:47:32 PDT)
- M. Reza Ganjalikhany (Sat Jul 25 2015 - 08:50:27 PDT)
- Ross Walker (Sat Jul 25 2015 - 07:59:16 PDT)
- M. Reza Ganjalikhany (Sat Jul 25 2015 - 04:48:36 PDT)
[AMBER] GTX Titan Xs slowing down after 200ns
- David A Case (Thu Jul 23 2015 - 11:14:17 PDT)
- Ross Walker (Thu Jul 23 2015 - 09:05:01 PDT)
- Mohamed Faizan Momin (Thu Jul 23 2015 - 08:46:11 PDT)
- Scott Le Grand (Thu Jul 23 2015 - 08:39:28 PDT)
- Mohamed Faizan Momin (Thu Jul 23 2015 - 08:26:42 PDT)
- Scott Le Grand (Thu Jul 23 2015 - 08:12:15 PDT)
- Ross Walker (Thu Jul 23 2015 - 07:51:31 PDT)
- Mohamed Faizan Momin (Thu Jul 23 2015 - 07:47:34 PDT)
- Ross Walker (Thu Jul 23 2015 - 07:41:12 PDT)
- Mohamed Faizan Momin (Thu Jul 23 2015 - 07:12:37 PDT)
[AMBER] GTX980Ti's now supported for AMBER and Exxact GTX780Tis available at discounted prices
- David Abia (Tue Jul 21 2015 - 03:15:34 PDT)
- Albert (Tue Jul 21 2015 - 02:11:12 PDT)
- Ross Walker (Mon Jul 20 2015 - 17:16:54 PDT)
[AMBER] hbond cpptraj
- Daniel Roe (Tue Jul 21 2015 - 13:34:15 PDT)
- Lara rajam (Tue Jul 21 2015 - 08:26:31 PDT)
[AMBER] help in amber
- Jason Swails (Wed Jul 08 2015 - 06:13:46 PDT)
- Robin Jain (Wed Jul 08 2015 - 02:31:26 PDT)
[AMBER] help in box size determination
- David A Case (Mon Jul 20 2015 - 07:24:54 PDT)
- Robin Jain (Sun Jul 19 2015 - 22:08:33 PDT)
[AMBER] help in box size detremination
- Robin Jain (Sun Jul 19 2015 - 02:19:04 PDT)
[AMBER] help in make .prepin file
- David A Case (Fri Jul 03 2015 - 05:22:16 PDT)
- Robin Jain (Fri Jul 03 2015 - 00:06:00 PDT)
[AMBER] help in making xyz file
- David A Case (Tue Jul 14 2015 - 05:31:40 PDT)
- Jason Swails (Tue Jul 14 2015 - 05:24:43 PDT)
- Robin Jain (Tue Jul 14 2015 - 02:14:01 PDT)
[AMBER] help in resp charge
- hannes.loeffler.stfc.ac.uk (Sat Jul 18 2015 - 01:05:29 PDT)
- Robin Jain (Sat Jul 18 2015 - 00:16:50 PDT)
[AMBER] how to center on ligand?
- Daniel Roe (Thu Jul 30 2015 - 04:16:52 PDT)
- Albert (Wed Jul 29 2015 - 23:08:16 PDT)
- Jason Swails (Wed Jul 29 2015 - 09:05:50 PDT)
- Albert (Wed Jul 29 2015 - 08:50:38 PDT)
- Daniel Roe (Wed Jul 29 2015 - 07:49:00 PDT)
- Jason Swails (Wed Jul 29 2015 - 07:28:30 PDT)
- Albert (Wed Jul 29 2015 - 07:25:35 PDT)
[AMBER] How to combine distance and torsion restraint?
- Jason Swails (Mon Jul 27 2015 - 06:54:32 PDT)
- Michael Shokhen (Mon Jul 27 2015 - 06:16:30 PDT)
[AMBER] How to set interatomic distance restraint?
- Michael Shokhen (Thu Jul 09 2015 - 01:18:40 PDT)
- Jason Swails (Mon Jul 06 2015 - 09:00:00 PDT)
- Michael Shokhen (Mon Jul 06 2015 - 08:43:08 PDT)
- David A Case (Sun Jul 05 2015 - 06:06:09 PDT)
- Michael Shokhen (Sun Jul 05 2015 - 05:04:46 PDT)
- David A Case (Fri Jul 03 2015 - 05:26:56 PDT)
- Michael Shokhen (Fri Jul 03 2015 - 00:19:37 PDT)
[AMBER] illegal memory access in amber GPU simulations
- Ross Walker (Fri Jul 17 2015 - 21:22:52 PDT)
- Latorraca, Naomi Rose (Fri Jul 17 2015 - 19:48:47 PDT)
[AMBER] Immediate Postdoctoral Position Opening In Dr. Khaled Barakat’s Lab, Faculty Of Pharmacy, University Of Alberta
- Ayesha Fatima (Tue Jul 21 2015 - 00:26:02 PDT)
[AMBER] impose restraint mask for specific residues
- Jason Swails (Fri Jul 24 2015 - 12:30:04 PDT)
- Latorraca, Naomi Rose (Fri Jul 24 2015 - 11:09:02 PDT)
[AMBER] incorrect determination of atomic number for atom Cl in tleap
- David A Case (Mon Jul 20 2015 - 07:31:16 PDT)
- Ye Renlo (Mon Jul 20 2015 - 06:32:15 PDT)
[AMBER] installation without ambertools
- Jason Swails (Mon Jul 20 2015 - 07:29:31 PDT)
- Asmita Gupta (Mon Jul 20 2015 - 01:17:03 PDT)
[AMBER] issue using CUDA+MPI+OpenMP
- Scott Le Grand (Thu Jul 09 2015 - 07:47:24 PDT)
- Jason Swails (Thu Jul 09 2015 - 06:06:51 PDT)
- Brent Krueger (Thu Jul 09 2015 - 05:40:45 PDT)
- Ross Walker (Thu Jul 09 2015 - 04:27:58 PDT)
- Éric Germaneau (Wed Jul 08 2015 - 17:33:57 PDT)
- David A Case (Wed Jul 08 2015 - 17:26:49 PDT)
- Éric Germaneau (Wed Jul 08 2015 - 17:02:08 PDT)
- Gerald Monard (Wed Jul 08 2015 - 01:10:42 PDT)
- Éric Germaneau (Tue Jul 07 2015 - 23:12:45 PDT)
[AMBER] Issues with running simulation after ParmEd conversion
- Rohith Mohan (Fri Jul 31 2015 - 13:49:14 PDT)
- Jason Swails (Thu Jul 30 2015 - 13:53:14 PDT)
- Rohith Mohan (Thu Jul 30 2015 - 13:06:11 PDT)
- Jason Swails (Wed Jul 29 2015 - 18:30:26 PDT)
- Rohith Mohan (Wed Jul 29 2015 - 14:06:47 PDT)
- Jason Swails (Wed Jul 29 2015 - 06:49:44 PDT)
- Rohith Mohan (Tue Jul 28 2015 - 16:30:26 PDT)
[AMBER] kclust help
- Daniel Roe (Thu Jul 02 2015 - 10:08:11 PDT)
- Harmeet Kaur (Thu Jul 02 2015 - 05:00:37 PDT)
[AMBER] leap changes residue order
- Ignacio Faustino (Thu Jul 02 2015 - 09:51:58 PDT)
- Jason Swails (Wed Jul 01 2015 - 09:14:17 PDT)
- Hannes Loeffler (Wed Jul 01 2015 - 09:12:05 PDT)
- Ignacio Faustino (Wed Jul 01 2015 - 09:04:37 PDT)
[AMBER] Lipid diffusion in cpptraj
- hannes.loeffler.stfc.ac.uk (Thu Jul 30 2015 - 23:42:35 PDT)
- Life Sciences Inc (Thu Jul 30 2015 - 14:22:16 PDT)
- Daniel Roe (Tue Jul 14 2015 - 07:40:45 PDT)
- hannes.loeffler.stfc.ac.uk (Mon Jul 13 2015 - 23:42:40 PDT)
- Life Sciences Inc (Mon Jul 13 2015 - 14:50:54 PDT)
- Daniel Roe (Thu Jul 09 2015 - 08:15:59 PDT)
- Life Sciences Inc (Wed Jul 08 2015 - 15:45:45 PDT)
- Daniel Roe (Thu Jul 02 2015 - 09:36:20 PDT)
- Life Sciences Inc (Wed Jul 01 2015 - 07:11:56 PDT)
[AMBER] Lipid linked to a peptide
- David A Case (Tue Jul 07 2015 - 10:23:46 PDT)
- Arnoult, Eric [JRDUS] (Tue Jul 07 2015 - 09:57:48 PDT)
[AMBER] Magnesium in MMGBSA
- Jason Swails (Fri Jul 10 2015 - 04:55:48 PDT)
- Ahmed Ayoub (Thu Jul 09 2015 - 19:27:53 PDT)
[AMBER] MCPB.py mismatch error
- Pengfei Li (Fri Jul 31 2015 - 13:50:30 PDT)
- Pengfei Li (Tue Jul 28 2015 - 20:26:56 PDT)
- Eleftherios A P Lambros (Mon Jul 27 2015 - 12:36:35 PDT)
[AMBER] MCPB.py N terminal error
- Takeshi Baba (Tue Jul 21 2015 - 07:34:19 PDT)
- Jon Uranga (Tue Jul 21 2015 - 06:21:52 PDT)
[AMBER] MCPB.py Value / Syntax error
- Pengfei Li (Wed Jul 22 2015 - 14:18:24 PDT)
- Eleftherios A P Lambros (Mon Jul 20 2015 - 18:13:25 PDT)
[AMBER] MCPB.py ValueError
- Takeshi Baba (Thu Jul 16 2015 - 19:01:28 PDT)
- Eleftherios A P Lambros (Thu Jul 16 2015 - 18:48:03 PDT)
[AMBER] MD simulation: cis isomer of peptide bond
- Michael Shokhen (Sun Jul 26 2015 - 12:00:51 PDT)
- Carlos Simmerling (Sun Jul 26 2015 - 11:24:33 PDT)
- Michael Shokhen (Sun Jul 26 2015 - 11:21:13 PDT)
- Carlos Simmerling (Sun Jul 26 2015 - 10:49:38 PDT)
- Michael Shokhen (Sun Jul 26 2015 - 10:34:38 PDT)
- Carlos Simmerling (Sun Jul 26 2015 - 09:43:23 PDT)
- Michael Shokhen (Sun Jul 26 2015 - 09:07:07 PDT)
[AMBER] mdfrc units
- Jason Swails (Fri Jul 31 2015 - 06:58:12 PDT)
- Georgios Gerogiokas (Fri Jul 31 2015 - 06:41:04 PDT)
[AMBER] MM-GBSA at different temperature
- Jason Swails (Wed Jul 29 2015 - 07:05:19 PDT)
- Shruti Koulgi (Tue Jul 28 2015 - 23:02:00 PDT)
[AMBER] MMPBSA.py API quasi-harmonic error
- D.J. Pattinson (Wed Jul 15 2015 - 01:36:03 PDT)
[AMBER] molecules split apart during MD
- Kenneth Huang (Fri Jul 10 2015 - 07:39:42 PDT)
- Jason Swails (Fri Jul 10 2015 - 07:37:29 PDT)
- Lara rajam (Fri Jul 10 2015 - 07:20:43 PDT)
[AMBER] Monitoring GPU voltage
- Ross Walker (Wed Jul 22 2015 - 17:57:43 PDT)
- Tru Huynh (Wed Jul 22 2015 - 13:01:49 PDT)
- Tru Huynh (Wed Jul 22 2015 - 12:52:30 PDT)
[AMBER] MPI compiling failed
- Jason Swails (Wed Jul 15 2015 - 10:29:29 PDT)
- Albert (Wed Jul 15 2015 - 05:10:55 PDT)
- David A Case (Wed Jul 15 2015 - 04:50:00 PDT)
- Albert (Wed Jul 15 2015 - 02:32:11 PDT)
[AMBER] MPI_ABORT error
- Jason Swails (Fri Jul 24 2015 - 13:56:01 PDT)
- Amber mail (Fri Jul 24 2015 - 12:41:17 PDT)
- Jason Swails (Fri Jul 24 2015 - 12:24:36 PDT)
- Amber mail (Fri Jul 24 2015 - 06:43:52 PDT)
- Jason Swails (Fri Jul 24 2015 - 06:28:11 PDT)
- Amber mail (Fri Jul 24 2015 - 05:33:12 PDT)
- Amber mail (Fri Jul 24 2015 - 05:28:02 PDT)
[AMBER] multiple cpus per single gpu job
- Meij, Henk (Thu Jul 30 2015 - 10:04:48 PDT)
- Ross Walker (Thu Jul 30 2015 - 09:06:37 PDT)
- Meij, Henk (Thu Jul 30 2015 - 08:11:13 PDT)
[AMBER] Mutation of a protein residue in TI computation with pmemd.MPI
- hannes.loeffler.stfc.ac.uk (Sat Jul 18 2015 - 02:00:26 PDT)
- Olivia Pierce (Fri Jul 17 2015 - 16:36:34 PDT)
- hannes.loeffler.stfc.ac.uk (Fri Jul 17 2015 - 13:35:02 PDT)
- Olivia Pierce (Fri Jul 17 2015 - 12:57:13 PDT)
- hannes.loeffler.stfc.ac.uk (Fri Jul 17 2015 - 10:22:22 PDT)
- Olivia Pierce (Fri Jul 17 2015 - 09:52:02 PDT)
- hannes.loeffler.stfc.ac.uk (Thu Jul 16 2015 - 23:30:40 PDT)
- Daniel Mermelstein (Thu Jul 16 2015 - 16:42:12 PDT)
- M Olivia Kim (Thu Jul 16 2015 - 15:13:06 PDT)
[AMBER] Namdenergy problems with non-standard amino acids
- Jason Swails (Thu Jul 09 2015 - 05:04:08 PDT)
- Clavel (Thu Jul 09 2015 - 02:34:53 PDT)
[AMBER] NetCDF file
- Hannes Loeffler (Wed Jul 15 2015 - 07:47:22 PDT)
- Marcus Arieno (Wed Jul 15 2015 - 07:34:51 PDT)
- Hai Nguyen (Wed Jul 15 2015 - 07:34:35 PDT)
- Hannes Loeffler (Wed Jul 15 2015 - 07:33:46 PDT)
- Marta Wisniewska (Wed Jul 15 2015 - 07:21:16 PDT)
[AMBER] NMR restraints with pmemd.cuda problem
- Ross Walker (Thu Jul 30 2015 - 07:54:56 PDT)
- Needham, Perri (Thu Jul 16 2015 - 12:34:18 PDT)
[AMBER] no FINAL_RESULTS_MMPBSA.dat generated
- Jason Swails (Fri Jul 17 2015 - 12:54:22 PDT)
- Albert (Fri Jul 17 2015 - 05:46:23 PDT)
[AMBER] NOESY volumes restraints
- David A Case (Mon Jul 13 2015 - 04:50:01 PDT)
- Eugene Sviridov (Fri Jul 10 2015 - 03:39:02 PDT)
- David A Case (Mon Jul 06 2015 - 07:42:02 PDT)
- Eugene Sviridov (Mon Jul 06 2015 - 04:08:30 PDT)
[AMBER] NumPy Import Error for MCPB.py on Amber15
- Hai Nguyen (Tue Jul 07 2015 - 17:10:57 PDT)
- Takeshi Baba (Tue Jul 07 2015 - 16:39:25 PDT)
- Eleftherios A P Lambros (Tue Jul 07 2015 - 16:23:54 PDT)
[AMBER] Order of the atom in prep ourput of antechamber
- David A Case (Sat Jul 11 2015 - 05:23:44 PDT)
- Thomas Fox (Fri Jul 10 2015 - 02:54:38 PDT)
- Hannes Loeffler (Fri Jul 10 2015 - 02:01:52 PDT)
- Nicholus Bhattacharjee (Fri Jul 10 2015 - 01:52:24 PDT)
[AMBER] Output format in sander
- John Dood (Thu Jul 02 2015 - 10:24:19 PDT)
- Jason Swails (Wed Jul 01 2015 - 09:00:17 PDT)
- Jason Swails (Wed Jul 01 2015 - 08:55:59 PDT)
- David A Case (Wed Jul 01 2015 - 05:38:05 PDT)
- Jason Swails (Wed Jul 01 2015 - 03:16:15 PDT)
- Brent Krueger (Tue Jun 30 2015 - 21:38:53 PDT)
[AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated.
- giulia palermo (Thu Jul 09 2015 - 08:47:35 PDT)
- Brent Krueger (Thu Jul 09 2015 - 03:45:21 PDT)
- FyD (Thu Jul 09 2015 - 01:44:28 PDT)
- giulia palermo (Wed Jul 08 2015 - 07:20:56 PDT)
- Jason Swails (Wed Jul 08 2015 - 06:11:02 PDT)
- giulia palermo (Wed Jul 08 2015 - 01:14:39 PDT)
[AMBER] parameters dATP
- Francesca Cardamone (Thu Jul 09 2015 - 06:07:07 PDT)
[AMBER] PCA and motions visualization
- Daniel Roe (Tue Jul 21 2015 - 16:04:55 PDT)
- Jason Swails (Tue Jul 21 2015 - 09:20:20 PDT)
- antonio.coluccia.uniroma1.it (Tue Jul 21 2015 - 02:59:54 PDT)
[AMBER] Periodic Box Size and Charge Determination
- David A Case (Wed Jul 22 2015 - 09:51:29 PDT)
- Aronica, Pietro (Wed Jul 22 2015 - 08:02:23 PDT)
- Jason Swails (Wed Jul 22 2015 - 06:06:10 PDT)
- Aronica, Pietro (Wed Jul 22 2015 - 05:43:46 PDT)
- Jason Swails (Wed Jul 22 2015 - 05:22:39 PDT)
- Aronica, Pietro (Wed Jul 22 2015 - 04:31:11 PDT)
[AMBER] PME large NFFT
- Jason Swails (Mon Jul 06 2015 - 08:15:33 PDT)
- John Dood (Mon Jul 06 2015 - 06:18:47 PDT)
[AMBER] pmemd.cuda implementation of sgld
- Daniel Roe (Sat Jul 11 2015 - 06:41:53 PDT)
- Asmita Gupta (Sat Jul 11 2015 - 00:50:31 PDT)
[AMBER] pmemd.cuda.MPI error - integer divide by zero
- Bill Miller III (Tue Jul 14 2015 - 18:11:34 PDT)
- Jason Swails (Sat Jul 11 2015 - 05:27:58 PDT)
- David A Case (Fri Jul 10 2015 - 17:03:12 PDT)
- Bill Miller III (Fri Jul 10 2015 - 14:36:38 PDT)
[AMBER] Prep file for chiral position
- Carlos Simmerling (Mon Jul 27 2015 - 10:54:29 PDT)
- Nicholus Bhattacharjee (Mon Jul 27 2015 - 10:37:14 PDT)
- Carlos Simmerling (Mon Jul 27 2015 - 10:07:44 PDT)
- Nicholus Bhattacharjee (Mon Jul 27 2015 - 09:51:56 PDT)
[AMBER] Problem cpptraj Bridging H-Bond analysis
- Daniel Roe (Mon Jul 20 2015 - 10:32:23 PDT)
- Beuerle, Matthias (Mon Jul 20 2015 - 06:52:22 PDT)
[AMBER] problem in amber
- Jason Swails (Thu Jul 09 2015 - 04:52:00 PDT)
- Robin Jain (Thu Jul 09 2015 - 00:32:05 PDT)
[AMBER] Problem in loading the pdb file
- Jason Swails (Fri Jul 10 2015 - 03:49:46 PDT)
- Harshala Haldankar (Thu Jul 09 2015 - 21:39:03 PDT)
- Jason Swails (Thu Jul 09 2015 - 05:23:54 PDT)
- Harshala Haldankar (Thu Jul 09 2015 - 03:58:07 PDT)
[AMBER] Problem in saving parameter/topology and coordinate file.
- David A Case (Tue Jul 21 2015 - 05:53:08 PDT)
- Bill Ross (Mon Jul 20 2015 - 13:11:46 PDT)
- Harshala Haldankar (Mon Jul 20 2015 - 04:34:07 PDT)
- Bill Ross (Sat Jul 18 2015 - 00:13:46 PDT)
- Harshala Haldankar (Fri Jul 17 2015 - 22:44:47 PDT)
[AMBER] Problem in Using the Average Command in Cpptraj
- Robert Molt (Mon Jul 13 2015 - 09:12:38 PDT)
- Daniel Roe (Mon Jul 13 2015 - 09:04:43 PDT)
- Jason Swails (Mon Jul 13 2015 - 09:04:35 PDT)
- Robert Molt (Mon Jul 13 2015 - 08:38:15 PDT)
[AMBER] problems on amoeba force filed implemented in amber
- Brian Radak (Wed Jul 15 2015 - 09:53:17 PDT)
- fjliu (Tue Jul 14 2015 - 19:43:32 PDT)
- Jason Swails (Tue Jul 14 2015 - 05:11:54 PDT)
- fjliu (Tue Jul 14 2015 - 02:35:30 PDT)
- Jason Swails (Fri Jul 10 2015 - 04:54:04 PDT)
- fjliu (Fri Jul 10 2015 - 01:53:01 PDT)
[AMBER] Producing Decoys with AmberTools
- Mohsen Zakeri (Sun Jul 12 2015 - 12:49:25 PDT)
[AMBER] qm-mmgbsa error
- Ayesha Fatima (Tue Jul 21 2015 - 22:59:19 PDT)
- Jason Swails (Tue Jul 21 2015 - 18:27:16 PDT)
- Ayesha Fatima (Tue Jul 21 2015 - 18:19:52 PDT)
- Jason Swails (Tue Jul 21 2015 - 09:23:20 PDT)
- Ayesha Fatima (Mon Jul 20 2015 - 21:55:17 PDT)
[AMBER] QM/GBSA calculation failed
- Jason Swails (Wed Jul 22 2015 - 07:31:00 PDT)
- Albert (Wed Jul 22 2015 - 07:24:57 PDT)
- Jason Swails (Wed Jul 22 2015 - 04:38:37 PDT)
- Albert (Wed Jul 22 2015 - 00:25:17 PDT)
[AMBER] QM/MM Equilibration Troubles
- Brian Radak (Wed Jul 01 2015 - 11:31:27 PDT)
- Brittany Boykin (Wed Jul 01 2015 - 11:00:11 PDT)
[AMBER] Query about adding hydrogens
- Bill Ross (Sat Jul 11 2015 - 15:20:41 PDT)
- anu chandra (Sat Jul 11 2015 - 13:08:54 PDT)
[AMBER] question about advanced tutorial 3
- Juan Eiros Zamora (Fri Jul 10 2015 - 03:30:29 PDT)
- Mohsen Zakeri (Fri Jul 10 2015 - 03:12:03 PDT)
[AMBER] Question about AMBER energy decomposition
- Jason Swails (Sat Jul 04 2015 - 16:00:18 PDT)
- Lee-Ping Wang (Sat Jul 04 2015 - 06:41:04 PDT)
- Jason Swails (Fri Jul 03 2015 - 14:30:00 PDT)
- Lee-Ping Wang (Fri Jul 03 2015 - 12:28:53 PDT)
[AMBER] Reference energies for Explicit solvent CpHMD
- Jason Swails (Mon Jul 06 2015 - 11:09:19 PDT)
- Arjun Sharma (Mon Jul 06 2015 - 10:33:36 PDT)
[AMBER] Regarding ADP molecule force fields
- Jason Swails (Fri Jul 31 2015 - 05:19:26 PDT)
- Yogeeshwar Ajjugal (Fri Jul 31 2015 - 02:41:24 PDT)
[AMBER] Regarding melt curve
- nhai.wn (Thu Jul 02 2015 - 21:26:12 PDT)
- MOHD HOMAIDUR RAHMAN (Thu Jul 02 2015 - 21:16:31 PDT)
[AMBER] Relaxing a heme molecule
- Amber Maharaj (Wed Jul 15 2015 - 12:26:49 PDT)
- case (Mon Jul 13 2015 - 17:35:19 PDT)
- Amber Maharaj (Mon Jul 13 2015 - 13:02:17 PDT)
[AMBER] RESP Fit to Atomic Multipoles
- Yip Yew Mun (Thu Jul 16 2015 - 08:30:53 PDT)
- ymei (Thu Jul 16 2015 - 08:18:54 PDT)
- Yip Yew Mun (Thu Jul 16 2015 - 08:01:46 PDT)
[AMBER] Restart of MMPBSA
- Jason Swails (Tue Jul 28 2015 - 11:11:39 PDT)
- Osman, Roman (Tue Jul 28 2015 - 11:09:29 PDT)
[AMBER] Rms fitting to a reference structure with a differnt number atoms to top file
- George Green (Wed Jul 01 2015 - 02:35:04 PDT)
[AMBER] running sgld in explicit solvent
- Asmita Gupta (Thu Jul 16 2015 - 07:28:23 PDT)
- David A Case (Thu Jul 16 2015 - 05:48:15 PDT)
- Asmita Gupta (Thu Jul 16 2015 - 04:01:48 PDT)
[AMBER] setting up a MD simulation using AMBER
- David A Case (Wed Jul 15 2015 - 08:41:18 PDT)
- Amber mail (Wed Jul 15 2015 - 06:11:10 PDT)
[AMBER] Solvents that are not in a list.
- Sharapa (Thu Jul 30 2015 - 04:16:55 PDT)
[AMBER] Speed of heating MD
- Amber mail (Sun Jul 26 2015 - 04:20:33 PDT)
- Jason Swails (Sat Jul 25 2015 - 17:51:44 PDT)
- Amber mail (Sat Jul 25 2015 - 02:32:33 PDT)
[AMBER] strange output from vacuum minimization
- David A Case (Wed Jul 15 2015 - 04:42:07 PDT)
- Albert (Wed Jul 15 2015 - 01:30:48 PDT)
[AMBER] strange pbsa results
- Jason Swails (Mon Jul 27 2015 - 06:32:55 PDT)
- Albert (Mon Jul 27 2015 - 02:54:45 PDT)
[AMBER] svdcmp in sander/ncsu-rmsd.F90 (AmberTools15) is sensitive to higher optimizations, suggest using lapack routine instead
- Åke Sandgren (Thu Jul 16 2015 - 10:05:29 PDT)
- David A Case (Thu Jul 16 2015 - 09:30:18 PDT)
[AMBER] Targeted Molecular dynamics in Amber
- Carlos Simmerling (Wed Jul 29 2015 - 07:12:57 PDT)
- ROOPALI VERMA (Mon Jul 27 2015 - 03:00:43 PDT)
[AMBER] test failed but still work
- Albert (Thu Jul 16 2015 - 06:46:40 PDT)
- David A Case (Thu Jul 16 2015 - 05:37:46 PDT)
- Albert (Wed Jul 15 2015 - 23:36:31 PDT)
- case (Wed Jul 15 2015 - 14:51:22 PDT)
- Albert (Wed Jul 15 2015 - 10:53:17 PDT)
- Albert (Wed Jul 15 2015 - 10:43:22 PDT)
- Jason Swails (Wed Jul 15 2015 - 10:32:44 PDT)
- David A Case (Wed Jul 15 2015 - 08:35:55 PDT)
- Albert (Wed Jul 15 2015 - 05:31:47 PDT)
[AMBER] Testing the titratable group definition CpHMD
- Jason Swails (Tue Jul 21 2015 - 09:13:58 PDT)
- Arjun Sharma (Tue Jul 21 2015 - 08:22:55 PDT)
[AMBER] Unchanged coordinates in leap
- mish (Wed Jul 22 2015 - 07:44:30 PDT)
- David A Case (Tue Jul 21 2015 - 06:05:50 PDT)
- mish (Tue Jul 21 2015 - 02:13:07 PDT)
[AMBER] Unexpected prochirality change from si to re during MD simulation
- David A Case (Mon Jul 13 2015 - 05:13:31 PDT)
- Michael Shokhen (Thu Jul 09 2015 - 01:28:59 PDT)
[AMBER] Using TIP4PEW amber FF in NAMD
- peter.schmidtke.discngine.servier.com (Fri Jul 24 2015 - 05:13:18 PDT)
- peter.schmidtke.discngine.servier.com (Fri Jul 24 2015 - 01:27:34 PDT)
[AMBER] Utilization of 3 GPUs suddenly drop to 0% and won't work any more
- Ross Walker (Fri Jul 31 2015 - 09:00:41 PDT)
- 浅井賢 (Thu Jul 30 2015 - 23:36:37 PDT)
- Ross Walker (Wed Jul 29 2015 - 07:31:45 PDT)
- 浅井賢 (Tue Jul 28 2015 - 23:35:38 PDT)
[AMBER] water networks and bridge option of the hbond command in cpptraj
- Daniel Roe (Thu Jul 02 2015 - 09:49:45 PDT)
- Vlad Cojocaru (Wed Jul 01 2015 - 10:44:49 PDT)
[AMBER] which solvent model to use with solvateCap
- Jason Swails (Mon Jul 27 2015 - 07:35:25 PDT)
- peter.schmidtke.discngine.servier.com (Mon Jul 27 2015 - 07:23:26 PDT)
- Jason Swails (Mon Jul 27 2015 - 07:19:10 PDT)
- peter.schmidtke.discngine.servier.com (Mon Jul 27 2015 - 04:12:18 PDT)
[AMBER] Why the entropy contribution from quasi-harmonic and normal mode methods are so different?
- wliu (Wed Jul 01 2015 - 21:19:47 PDT)
- Hannes Loeffler (Wed Jul 01 2015 - 02:52:11 PDT)
- wliu (Wed Jul 01 2015 - 02:13:54 PDT)

Amber Archive Jul 2015 by subject