Amber Archive Feb 2017: by subject

[AMBER-Developers] [AMBER] problems with heating
- David Case (Wed Feb 22 2017 - 18:26:12 PST)
[AMBER-Developers] [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue
- David Case (Fri Feb 24 2017 - 04:54:24 PST)
[AMBER-Developers] [AMBER] Velocity file output AMBER16
- David Case (Sat Feb 18 2017 - 12:34:09 PST)
[AMBER-Developers] [AMBER] 回复： Using CHARMM 36 force field in AMBER
- David Case (Thu Feb 23 2017 - 05:28:52 PST)
[AMBER] 12-6-4 potential in TI
- Qinghua Liao (Tue Feb 21 2017 - 02:09:00 PST)
- Hannes Loeffler (Tue Feb 21 2017 - 01:06:03 PST)
- Qinghua Liao (Mon Feb 20 2017 - 14:37:24 PST)
[AMBER] 8 GPU single pmemd run with amber 16?
- Chris Neale (Mon Feb 06 2017 - 13:09:28 PST)
- Scott Le Grand (Mon Feb 06 2017 - 12:59:33 PST)
- Ross Walker (Mon Feb 06 2017 - 12:56:13 PST)
- Chris Neale (Mon Feb 06 2017 - 12:31:12 PST)
[AMBER] > source leaprc.water.tip3p
- David Case (Tue Feb 21 2017 - 11:05:22 PST)
- chemocev marker (Tue Feb 21 2017 - 07:17:01 PST)
- David Case (Tue Feb 21 2017 - 06:28:05 PST)
- chemocev marker (Tue Feb 21 2017 - 05:35:57 PST)
[AMBER] [Amber] Frequencies from normal mode analysis in nab
- James Kress (Sun Feb 19 2017 - 10:07:15 PST)
- David Case (Sat Feb 18 2017 - 12:33:57 PST)
- The Cromicus Productions (Tue Feb 14 2017 - 00:03:38 PST)
[AMBER] [MMPBSA.py.MPI] Two questions (autoimage and parsing of output)
- Eiros Zamora, Juan (Mon Feb 06 2017 - 06:30:11 PST)
- Eiros Zamora, Juan (Mon Feb 06 2017 - 04:16:26 PST)
- Eiros Zamora, Juan (Fri Feb 03 2017 - 08:11:01 PST)
- Jason Swails (Fri Feb 03 2017 - 05:06:23 PST)
- Daniel Roe (Thu Feb 02 2017 - 06:52:24 PST)
- Eiros Zamora, Juan (Wed Feb 01 2017 - 05:09:02 PST)
[AMBER] [q4md-fft] Unknown parameters frcmod.unknown
- FyD (Sun Feb 26 2017 - 02:05:02 PST)
[AMBER] ADDING WATER MOLECULES
- David Case (Sun Feb 05 2017 - 05:31:31 PST)
- Elvis Martis (Sat Feb 04 2017 - 03:18:34 PST)
- Subashini .K (Sat Feb 04 2017 - 02:54:49 PST)
[AMBER] Alternatives to ambmask that might work with parmed/gromber generated .prmtop files?
- Chris Neale (Thu Feb 23 2017 - 12:29:02 PST)
- Daniel Roe (Thu Feb 23 2017 - 11:38:50 PST)
- Chris Neale (Thu Feb 23 2017 - 10:13:16 PST)
[AMBER] AMBER 16 problem with LEaP's addIons command
- Nhai (Tue Feb 21 2017 - 15:05:34 PST)
- Kasprzak, Wojciech (NIH/NCI) [C] (Tue Feb 21 2017 - 14:58:11 PST)
- Hai Nguyen (Tue Feb 21 2017 - 13:23:22 PST)
- Kasprzak, Wojciech (NIH/NCI) [C] (Tue Feb 21 2017 - 13:20:31 PST)
[AMBER] AMBER Digest, Vol 1852, Issue 1
- Bill Ross (Tue Feb 21 2017 - 03:04:41 PST)
- Tiffani Rovira (Tue Feb 21 2017 - 02:41:48 PST)
[AMBER] Amber Energy Unit Meaning
- Ross Walker (Tue Feb 14 2017 - 04:40:45 PST)
- Bill Ross (Mon Feb 13 2017 - 23:06:03 PST)
- Bill Ross (Mon Feb 13 2017 - 23:02:29 PST)
- Eugene Cha (Mon Feb 13 2017 - 22:47:34 PST)
[AMBER] Amber force filed parameter
- David Case (Thu Feb 23 2017 - 05:22:48 PST)
- Statics Eng (Thu Feb 23 2017 - 04:29:29 PST)
- Bill Ross (Wed Feb 22 2017 - 15:13:42 PST)
- Bill Ross (Wed Feb 22 2017 - 14:58:32 PST)
- Adrian Roitberg (Wed Feb 22 2017 - 14:32:09 PST)
- Statics Eng (Wed Feb 22 2017 - 14:30:14 PST)
[AMBER] Amber15 Cpinutil.py Bug
- Jason Swails (Tue Feb 14 2017 - 19:39:20 PST)
- Chase Zagorec-Marks (Tue Feb 14 2017 - 13:19:09 PST)
[AMBER] Amber16 -mpt-2.15-gcc/6.1.0-RHEL7.3- compilation error
- Feng Pan (Thu Feb 16 2017 - 11:12:04 PST)
- Sudhakar Lakkaraju (Thu Feb 16 2017 - 09:23:50 PST)
- Sudhakar Lakkaraju (Thu Feb 09 2017 - 09:43:43 PST)
- Feng Pan (Thu Feb 09 2017 - 08:09:49 PST)
- Sudhakar Lakkaraju (Wed Feb 08 2017 - 09:56:14 PST)
- David Case (Wed Feb 08 2017 - 07:42:55 PST)
- Sudhakar Lakkaraju (Wed Feb 08 2017 - 07:07:58 PST)
[AMBER] Amber16 installation error
- David Case (Thu Feb 02 2017 - 05:17:59 PST)
- Nhai (Wed Feb 01 2017 - 22:47:19 PST)
- SeungHyun Kim (Wed Feb 01 2017 - 22:39:28 PST)
[AMBER] Antechamber Gaff Am1-bcc charges
- David Case (Thu Feb 23 2017 - 05:16:40 PST)
- Mitul Srivastava (Thu Feb 23 2017 - 00:38:43 PST)
- Neha Gandhi (Thu Feb 23 2017 - 00:22:07 PST)
[AMBER] antechamber warning
- Saman Yousuf ali (Wed Feb 22 2017 - 20:08:12 PST)
- Scott Brozell (Wed Feb 22 2017 - 11:22:58 PST)
- Saman Yousuf ali (Wed Feb 22 2017 - 00:11:57 PST)
- Scott Brozell (Tue Feb 21 2017 - 23:11:36 PST)
- Saman Yousuf ali (Tue Feb 21 2017 - 22:18:13 PST)
- Saman Yousuf ali (Tue Feb 21 2017 - 08:16:31 PST)
[AMBER] APR - atom selection
- Andreas Tosstorff (Tue Feb 07 2017 - 05:38:03 PST)
- Jian Yin (Thu Feb 02 2017 - 12:46:22 PST)
- Andreas Tosstorff (Wed Feb 01 2017 - 07:10:57 PST)
- Daniel Roe (Wed Feb 01 2017 - 06:52:56 PST)
- Andreas Tosstorff (Wed Feb 01 2017 - 05:05:56 PST)
[AMBER] binding energy decomposition
- Bruno Falcone (Fri Feb 03 2017 - 06:03:13 PST)
- Jacopo Sgrignani (Thu Feb 02 2017 - 12:44:37 PST)
[AMBER] binding free energy- error calculation
- Mary Varughese (Tue Feb 14 2017 - 21:01:57 PST)
[AMBER] binding free energy- error calculation doubt
- Elvis Martis (Wed Feb 22 2017 - 04:21:12 PST)
- Mary Varughese (Wed Feb 22 2017 - 03:00:02 PST)
- David Case (Tue Feb 21 2017 - 05:19:54 PST)
- Mary Varughese (Tue Feb 21 2017 - 02:08:15 PST)
[AMBER] building premed for Intel Xeon Phi coprocessors (offload mode)
- Song-Ho Chong (Tue Feb 14 2017 - 23:04:21 PST)
[AMBER] Call for awards applications for ACS COMP Division Fall meeting in DC
- Carlos Simmerling (Sat Feb 25 2017 - 03:08:05 PST)
[AMBER] cannot add bond
- Sowmya Indrakumar (Thu Feb 02 2017 - 00:49:20 PST)
- Elvis Martis (Wed Feb 01 2017 - 19:51:04 PST)
- Thakur, Abhishek (Wed Feb 01 2017 - 14:26:09 PST)
[AMBER] Cannot convert rst to pdb file after md simulation.
- Vatsal Purohit (Mon Feb 27 2017 - 10:54:52 PST)
- Daniel Roe (Mon Feb 27 2017 - 10:23:20 PST)
- Bill Ross (Mon Feb 27 2017 - 10:03:02 PST)
- Vatsal Purohit (Mon Feb 27 2017 - 09:52:04 PST)
- Daniel Roe (Mon Feb 27 2017 - 09:40:44 PST)
- Vatsal Purohit (Mon Feb 27 2017 - 09:29:13 PST)
[AMBER] Cannot open the main chain file after prepgen command
- David Case (Mon Feb 06 2017 - 08:08:00 PST)
- Nikolay N. Kuzmich (Mon Feb 06 2017 - 04:09:52 PST)
[AMBER] changing chirality with ParmEd?
- Carlos Simmerling (Tue Feb 21 2017 - 13:41:36 PST)
- Osman, Roman (Tue Feb 21 2017 - 13:39:13 PST)
- Hai Nguyen (Tue Feb 21 2017 - 13:39:06 PST)
- Carlos Simmerling (Tue Feb 21 2017 - 13:33:23 PST)
- Lachele Foley (Tue Feb 21 2017 - 13:26:32 PST)
- Hai Nguyen (Mon Feb 20 2017 - 11:42:18 PST)
- Thomas Pochapsky (Mon Feb 20 2017 - 07:14:48 PST)
[AMBER] changing water molecules in water box
- Lara rajam (Thu Feb 02 2017 - 13:07:45 PST)
- David Case (Thu Feb 02 2017 - 12:54:38 PST)
- Lara rajam (Thu Feb 02 2017 - 07:24:08 PST)
[AMBER] Charge error in Antechamber.
- Bruno Falcone (Fri Feb 24 2017 - 10:13:13 PST)
- Hannes Loeffler (Fri Feb 24 2017 - 09:36:25 PST)
- Vatsal Purohit (Fri Feb 24 2017 - 09:28:16 PST)
- Bruno Falcone (Fri Feb 24 2017 - 09:04:54 PST)
- Vatsal Purohit (Fri Feb 24 2017 - 08:50:57 PST)
[AMBER] CHARMM36 force field
- Dickson, Callum J (Fri Feb 10 2017 - 08:41:45 PST)
- Shanghaitech University WuMeng (Thu Feb 09 2017 - 05:08:38 PST)
[AMBER] clustering
- Daniel Roe (Thu Feb 02 2017 - 06:46:02 PST)
- Sowmya Indrakumar (Thu Feb 02 2017 - 00:46:57 PST)
- Ravi Abrol (Wed Feb 01 2017 - 15:08:37 PST)
- Sowmya Indrakumar (Wed Feb 01 2017 - 03:41:39 PST)
[AMBER] Compilation errors
- Jason Swails (Sun Feb 12 2017 - 18:37:39 PST)
- Sudhakar Lakkaraju (Sun Feb 12 2017 - 18:06:07 PST)
[AMBER] constant pH caluculations with pmemd.cuda.MPI
- Florian Hofer (Wed Feb 15 2017 - 06:19:34 PST)
- Adrian Roitberg (Wed Feb 15 2017 - 06:15:32 PST)
- Hofer, Florian (Wed Feb 15 2017 - 04:50:44 PST)
[AMBER] constrain nitrate as bound and neutral
- Pengfei Li (Wed Feb 01 2017 - 07:48:35 PST)
[AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds
- Eric Lang (Fri Feb 10 2017 - 02:34:56 PST)
- Jason Swails (Wed Feb 08 2017 - 19:19:24 PST)
- Eric Lang (Wed Feb 08 2017 - 04:16:24 PST)
- Adrian Roitberg (Tue Feb 07 2017 - 05:28:11 PST)
- Eric Lang (Tue Feb 07 2017 - 05:22:16 PST)
[AMBER] CPPTRAJ combined clustering with different topologies
- Daniel Roe (Mon Feb 13 2017 - 06:16:32 PST)
- Jan Ludwiczak (Mon Feb 13 2017 - 04:59:02 PST)
[AMBER] cpptraj: dihcovar and projection need trajin to work properly?
- Thomas Fox (Tue Feb 28 2017 - 07:33:54 PST)
[AMBER] cpptraj: dihcovar and projection need trajin to work properly? - FollowUp
- Thomas Fox (Tue Feb 28 2017 - 07:42:48 PST)
[AMBER] Creating a double bond in a pdb file with xleap
- Aseel Bala (Tue Feb 21 2017 - 08:40:21 PST)
- Aseel Bala (Tue Feb 21 2017 - 08:40:10 PST)
- Bill Ross (Thu Feb 16 2017 - 22:54:10 PST)
- Vaibhav Dixit (Thu Feb 16 2017 - 22:40:03 PST)
- David Case (Thu Feb 16 2017 - 13:50:32 PST)
- Aseel Bala (Thu Feb 16 2017 - 12:47:27 PST)
- David Case (Wed Feb 15 2017 - 18:31:24 PST)
- Aseel Bala (Wed Feb 15 2017 - 11:08:03 PST)
[AMBER] custom directory for DFTB parameter files
- Alfredo Quevedo (Thu Feb 09 2017 - 10:45:23 PST)
- Gustavo Seabra (Thu Feb 09 2017 - 10:37:23 PST)
- Alfredo Quevedo (Thu Feb 09 2017 - 07:41:36 PST)
[AMBER] density and concentration of 8Mureabox
- Jorge Iulek (Thu Feb 16 2017 - 08:44:18 PST)
[AMBER] DFTB3 in Amber is not there, but it may be in gromacs.
- Markus Kaukonen (Tue Feb 07 2017 - 03:04:17 PST)
[AMBER] Differences using leaprc.ff14SB from AmberTools15 and oldff/leaprc.ff14SB from AmberTools16
- Joao Damas (Wed Feb 01 2017 - 13:27:46 PST)
- Daniel Roe (Tue Jan 31 2017 - 17:27:18 PST)
[AMBER] DIMENSION OF BOX
- Daniel Roe (Thu Feb 23 2017 - 05:40:37 PST)
- Subashini .K (Thu Feb 23 2017 - 04:58:15 PST)
[AMBER] Distance between of each residues of two chains within trajectory
- Daniel Roe (Tue Feb 21 2017 - 08:52:03 PST)
- Jesmita Dhar (Mon Feb 20 2017 - 01:22:33 PST)
[AMBER] EPM2 Force field for CO2
- Liyang Zhu (Thu Feb 09 2017 - 15:42:21 PST)
- David Case (Thu Feb 09 2017 - 13:09:03 PST)
- Liyang Zhu (Thu Feb 09 2017 - 09:54:25 PST)
- David Case (Wed Feb 08 2017 - 16:17:14 PST)
- Liyang Zhu (Mon Feb 06 2017 - 13:28:43 PST)
- David Case (Mon Feb 06 2017 - 08:03:16 PST)
- Liyang Zhu (Sun Feb 05 2017 - 17:34:59 PST)
[AMBER] Error in compiling pmemd.cuda
- Ross Walker (Wed Feb 01 2017 - 20:15:21 PST)
- Ross Walker (Wed Feb 01 2017 - 20:14:28 PST)
- Elvis Martis (Wed Feb 01 2017 - 20:11:13 PST)
- Anton Perera (Wed Feb 01 2017 - 20:06:12 PST)
[AMBER] error in the input file
- Michael Shokhen (Mon Feb 20 2017 - 06:38:08 PST)
- Hannes Loeffler (Mon Feb 20 2017 - 05:58:44 PST)
- Qinghua Liao (Mon Feb 20 2017 - 05:51:16 PST)
- Michael Shokhen (Mon Feb 20 2017 - 05:47:09 PST)
- Bill Ross (Mon Feb 20 2017 - 05:36:25 PST)
- Michael Shokhen (Mon Feb 20 2017 - 05:31:26 PST)
- Bill Ross (Mon Feb 20 2017 - 05:23:08 PST)
- Michael Shokhen (Mon Feb 20 2017 - 05:11:57 PST)
- Bill Ross (Mon Feb 20 2017 - 04:50:26 PST)
- Michael Shokhen (Mon Feb 20 2017 - 04:47:03 PST)
[AMBER] Explicity solvent CpHD, -cprestrt .cpin file
- Eric Lang (Fri Feb 10 2017 - 13:10:00 PST)
- Tsibela German Tebello Mofokeng (Fri Feb 10 2017 - 07:33:12 PST)
- Eric Lang (Fri Feb 10 2017 - 06:56:17 PST)
- Tsibela German Tebello Mofokeng (Fri Feb 10 2017 - 06:40:18 PST)
[AMBER] Failed to calculate entropy with mm_pbsa.pl in AMBER14, with no error informations reported in nmode_com.1.out
- David Case (Thu Feb 09 2017 - 06:02:35 PST)
- Elvis Martis (Thu Feb 09 2017 - 04:08:37 PST)
- Hai Nguyen (Wed Feb 08 2017 - 20:49:05 PST)
- wei (Wed Feb 08 2017 - 20:36:47 PST)
[AMBER] Force Field for Ammonia?
- Gustavo Seabra (Mon Feb 06 2017 - 07:00:24 PST)
- jojartb.jgypk.u-szeged.hu (Fri Feb 03 2017 - 22:10:21 PST)
- Andrew Schaub (Fri Feb 03 2017 - 20:18:22 PST)
- Gustavo Seabra (Fri Feb 03 2017 - 08:37:44 PST)
[AMBER] Free energy calculation SHAKE's failure when heating.
- Hannes Loeffler (Sat Feb 25 2017 - 01:35:04 PST)
- Artem Shekhovtsov (Fri Feb 24 2017 - 11:06:00 PST)
- Hannes Loeffler (Fri Feb 24 2017 - 08:47:42 PST)
- Hannes Loeffler (Fri Feb 24 2017 - 08:35:23 PST)
- Artem Shekhovtsov (Fri Feb 24 2017 - 08:11:53 PST)
[AMBER] frequency contact maps
- Daniel Roe (Tue Feb 21 2017 - 07:16:06 PST)
- Antonio Coluccia (Tue Feb 21 2017 - 06:45:00 PST)
- Daniel Roe (Fri Feb 17 2017 - 06:48:19 PST)
- Antonio Coluccia (Fri Feb 17 2017 - 01:04:42 PST)
- Alejandro Sosa (Thu Feb 16 2017 - 13:38:27 PST)
- Antonio Coluccia (Wed Feb 15 2017 - 08:15:50 PST)
- Daniel Roe (Wed Feb 15 2017 - 07:38:57 PST)
- antonio.coluccia.uniroma1.it (Wed Feb 15 2017 - 06:28:05 PST)
[AMBER] Fwd: binding free energy- error calculation
- Hai Nguyen (Thu Feb 16 2017 - 19:19:57 PST)
- Mary Varughese (Thu Feb 16 2017 - 19:02:04 PST)
[AMBER] Fwd: Error during installation process
- David Case (Thu Feb 02 2017 - 05:21:34 PST)
- David Case (Thu Feb 02 2017 - 05:08:31 PST)
- Danu Fajar (Wed Feb 01 2017 - 18:03:57 PST)
- Danu Fajar (Tue Jan 31 2017 - 19:28:45 PST)
- Danu Fajar (Tue Jan 31 2017 - 09:46:54 PST)
- Danu Fajar (Tue Jan 31 2017 - 09:37:49 PST)
[AMBER] Fwd: SQM Error
- Bill Ross (Wed Feb 22 2017 - 01:00:22 PST)
- Bill Ross (Wed Feb 22 2017 - 00:54:44 PST)
- Goetz, Andreas (Wed Feb 22 2017 - 00:54:26 PST)
- Mitul Srivastava (Wed Feb 22 2017 - 00:45:30 PST)
- Bill Ross (Wed Feb 22 2017 - 00:40:30 PST)
- Mitul Srivastava (Wed Feb 22 2017 - 00:36:12 PST)
- Bill Ross (Wed Feb 22 2017 - 00:30:38 PST)
- Mitul Srivastava (Wed Feb 22 2017 - 00:28:48 PST)
- Bill Ross (Wed Feb 22 2017 - 00:27:11 PST)
- Mitul Srivastava (Wed Feb 22 2017 - 00:24:37 PST)
- Goetz, Andreas (Wed Feb 22 2017 - 00:09:05 PST)
- Bill Ross (Wed Feb 22 2017 - 00:05:14 PST)
- Mitul Srivastava (Wed Feb 22 2017 - 00:00:22 PST)
- Bill Ross (Tue Feb 21 2017 - 23:57:13 PST)
- Mitul Srivastava (Tue Feb 21 2017 - 23:52:04 PST)
- Goetz, Andreas (Tue Feb 21 2017 - 23:42:16 PST)
- Bill Ross (Tue Feb 21 2017 - 23:28:00 PST)
- Mitul Srivastava (Tue Feb 21 2017 - 22:53:01 PST)
[AMBER] Give the correct charge to heme using antechamber
- Matteo Uggeri (Wed Feb 01 2017 - 06:36:41 PST)
[AMBER] H_bond
- Daniel Roe (Mon Feb 13 2017 - 12:12:08 PST)
- Thakur, Abhishek (Sun Feb 12 2017 - 08:22:13 PST)
[AMBER] help in parameters
- David Case (Thu Feb 16 2017 - 05:11:43 PST)
- Bill Ross (Tue Feb 14 2017 - 22:32:21 PST)
- Robin Jain (Tue Feb 14 2017 - 22:08:34 PST)
[AMBER] How to define a "Dihedral parameters" crossing a C-C triple bond? (Due to two fragment's interaction)
- Siwei Wang (Fri Feb 24 2017 - 18:32:11 PST)
[AMBER] How to download patches and updates manually
- Jason Swails (Wed Feb 08 2017 - 19:24:10 PST)
- Hai Nguyen (Wed Feb 08 2017 - 08:52:35 PST)
- Chris Neale (Wed Feb 08 2017 - 07:56:29 PST)
- Elisa Pieri (Wed Feb 08 2017 - 07:49:21 PST)
[AMBER] how to solve syntax error issue
- David Case (Tue Feb 07 2017 - 05:50:43 PST)
- Elvis Martis (Tue Feb 07 2017 - 04:15:27 PST)
- Ayesha Kanwal (Tue Feb 07 2017 - 02:09:57 PST)
[AMBER] Hydrophobic and pi-pi interaction
- Thakur, Abhishek (Wed Feb 15 2017 - 07:40:14 PST)
[AMBER] IERR CPU hang needing support please
- Ross Walker (Fri Feb 17 2017 - 08:35:57 PST)
- Curtis Walker (Thu Feb 16 2017 - 14:11:17 PST)
[AMBER] Installation problem with miniconda
- ABHIJEET CHOWDHURY (Fri Feb 17 2017 - 04:53:15 PST)
- Hai Nguyen (Wed Feb 15 2017 - 10:09:04 PST)
- ABHIJEET CHOWDHURY (Wed Feb 15 2017 - 09:27:58 PST)
- Hai Nguyen (Wed Feb 15 2017 - 05:26:47 PST)
- ABHIJEET CHOWDHURY (Wed Feb 15 2017 - 05:13:36 PST)
[AMBER] LeAP and FFs for Hybrid DNA/RNA structure
- Hai Nguyen (Mon Feb 20 2017 - 11:46:02 PST)
- Kasprzak, Wojciech (NIH/NCI) [C] (Mon Feb 20 2017 - 10:36:18 PST)
- David Case (Sat Feb 18 2017 - 12:33:35 PST)
- Kasprzak, Wojciech (NIH/NCI) [C] (Fri Feb 17 2017 - 12:09:39 PST)
[AMBER] LES, Umbrella sampling and/or NEB
- Stregone (Thu Feb 16 2017 - 03:50:59 PST)
[AMBER] lj1264 pmemd.cuda
- Jason Swails (Sun Feb 05 2017 - 21:50:03 PST)
- Pengfei Li (Sat Feb 04 2017 - 14:20:55 PST)
- Jason Swails (Thu Feb 02 2017 - 18:27:23 PST)
[AMBER] makeDIST_RST issue
- Miguel Garavís (Fri Feb 17 2017 - 05:32:48 PST)
- David Case (Fri Feb 17 2017 - 05:24:03 PST)
- Miguel Garavís (Fri Feb 17 2017 - 04:29:00 PST)
[AMBER] Memory usage of NMR center of mass restreaints on GPUs
- paul (Tue Feb 21 2017 - 05:33:15 PST)
[AMBER] Methods to count the different species
- Liyang Zhu (Tue Feb 28 2017 - 10:59:53 PST)
- Daniel Roe (Thu Feb 02 2017 - 06:59:17 PST)
[AMBER] Minimisation error and system blowup for a large protein using implicit solvent
- Joseph Salmon (Thu Feb 23 2017 - 07:08:17 PST)
- Hai Nguyen (Wed Feb 22 2017 - 10:46:41 PST)
- Joseph Salmon (Wed Feb 22 2017 - 10:37:16 PST)
- Nhai (Wed Feb 22 2017 - 09:12:13 PST)
- Nhai (Wed Feb 22 2017 - 08:44:13 PST)
- Joseph Salmon (Wed Feb 22 2017 - 06:54:03 PST)
[AMBER] minimization issue (**** in rst file)
- David Case (Tue Feb 21 2017 - 05:15:23 PST)
- Chinh Su Tran To (Mon Feb 20 2017 - 23:18:53 PST)
- Bill Ross (Mon Feb 20 2017 - 22:28:26 PST)
- Bill Ross (Mon Feb 20 2017 - 22:19:23 PST)
- Chinh Su Tran To (Mon Feb 20 2017 - 21:55:14 PST)
- Bill Ross (Mon Feb 20 2017 - 19:50:52 PST)
- Hai Nguyen (Mon Feb 20 2017 - 19:33:27 PST)
- Chinh Su Tran To (Mon Feb 20 2017 - 19:07:46 PST)
[AMBER] MM energy contributions of atoms in a molecule
- Jas Kalayan (Mon Feb 27 2017 - 08:52:51 PST)
[AMBER] MMPBSA error
- konda003 . (Thu Feb 16 2017 - 12:02:35 PST)
- konda003 . (Mon Feb 06 2017 - 12:43:36 PST)
- Ray Luo (Mon Feb 06 2017 - 10:31:26 PST)
- konda003 . (Mon Feb 06 2017 - 09:08:42 PST)
[AMBER] MMPBSA failed
- Jason Swails (Wed Feb 08 2017 - 21:00:28 PST)
- Vlad Cojocaru (Wed Feb 01 2017 - 06:35:00 PST)
- Albert (Wed Feb 01 2017 - 06:18:38 PST)
- Vlad Cojocaru (Wed Feb 01 2017 - 04:37:32 PST)
- Albert (Wed Feb 01 2017 - 03:46:10 PST)
- Vlad Cojocaru (Wed Feb 01 2017 - 03:21:27 PST)
- Albert (Wed Feb 01 2017 - 03:11:12 PST)
- Albert (Tue Jan 31 2017 - 23:46:48 PST)
[AMBER] MTKpp.pdf manual
- Hai Nguyen (Thu Feb 02 2017 - 09:13:02 PST)
- Corum, Katharine W (Thu Feb 02 2017 - 09:11:42 PST)
- Pengfei Li (Thu Feb 02 2017 - 09:10:23 PST)
- Corum, Katharine W (Thu Feb 02 2017 - 09:08:19 PST)
[AMBER] Multiple ligands in MMGBSA
- Abhilash J (Thu Feb 02 2017 - 00:22:36 PST)
- Elvis Martis (Wed Feb 01 2017 - 04:29:57 PST)
- Abhilash J (Wed Feb 01 2017 - 02:39:06 PST)
- Elvis Martis (Tue Jan 31 2017 - 19:13:13 PST)
[AMBER] Na cation drifts away from metal chelating protein
- Michael Shokhen (Sun Feb 19 2017 - 02:59:11 PST)
- Bill Ross (Sun Feb 19 2017 - 02:49:09 PST)
- Elvis Martis (Sun Feb 19 2017 - 02:41:16 PST)
- Michael Shokhen (Sun Feb 19 2017 - 01:45:13 PST)
[AMBER] Non standrad residue unknown parameters and atomtypes
- Maral Aminpour (Fri Feb 24 2017 - 09:22:37 PST)
[AMBER] Number of threads in MMGBSA/MMPBSA calculations.
- Jason Swails (Mon Feb 06 2017 - 17:52:06 PST)
- Abhilash J (Sat Feb 04 2017 - 05:59:06 PST)
- Elvis Martis (Sat Feb 04 2017 - 00:25:57 PST)
- Abhilash J (Fri Feb 03 2017 - 22:27:05 PST)
[AMBER] Obtain dynamical matrix away from equilibrium
- Adrian Roitberg (Thu Feb 09 2017 - 10:10:48 PST)
- The Cromicus Productions (Thu Feb 09 2017 - 10:00:37 PST)
[AMBER] Parameters for nucelotides
- FyD (Fri Feb 03 2017 - 00:53:50 PST)
- Buteler,Maria del Pilar (Thu Feb 02 2017 - 08:15:12 PST)
[AMBER] parmed add12_6_4 command error
- Marek Havrila (Sat Feb 04 2017 - 14:25:14 PST)
- Pengfei Li (Sat Feb 04 2017 - 14:03:21 PST)
- Marek Havrila (Sat Feb 04 2017 - 13:41:19 PST)
[AMBER] parmed gromber issues inappropriate disulfide warning based on CYS/MET approach
- Chris Neale (Fri Feb 03 2017 - 13:57:39 PST)
[AMBER] ParmEd problem: LJ12_6_4Error: Could not find parameters for ATOM_TYPE CL
- Pengfei Li (Tue Feb 21 2017 - 13:33:46 PST)
- 杨金鹏 (Tue Feb 21 2017 - 05:42:20 PST)
[AMBER] pbsa EDISPER with radiopt=0 vs radiopt=1
- Ray Luo (Fri Feb 24 2017 - 08:35:37 PST)
- Paulo Costa (Fri Feb 24 2017 - 01:32:23 PST)
- Paulo Costa (Thu Feb 23 2017 - 06:57:40 PST)
[AMBER] PCA
- Daniel Roe (Mon Feb 13 2017 - 12:15:35 PST)
- Elvis Martis (Thu Feb 09 2017 - 17:26:36 PST)
- Thakur, Abhishek (Thu Feb 09 2017 - 14:20:48 PST)
[AMBER] PCA analysis
- Thakur, Abhishek (Thu Feb 09 2017 - 07:30:02 PST)
- Elvis Martis (Thu Feb 09 2017 - 07:06:41 PST)
- Elvis Martis (Thu Feb 09 2017 - 07:02:25 PST)
- Thakur, Abhishek (Thu Feb 09 2017 - 06:58:24 PST)
[AMBER] periodic boundary conditions
- Neha Gandhi (Mon Feb 27 2017 - 17:19:56 PST)
[AMBER] pi-pi interaction and hydrophobic
- Jiri Sponer (Sat Feb 25 2017 - 01:05:39 PST)
- Chris Neale (Fri Feb 24 2017 - 14:46:58 PST)
- Jianping Lin (Fri Feb 24 2017 - 14:35:08 PST)
- Kenneth McGuinness (Fri Feb 24 2017 - 14:17:40 PST)
- Thakur, Abhishek (Fri Feb 24 2017 - 12:59:02 PST)
[AMBER] PLUMED Meeting 2017
- Giovanni Bussi (Tue Feb 14 2017 - 01:03:01 PST)
[AMBER] pmemd.cuda.MPI not running well with SGE
- Wang, Yin (Tue Feb 14 2017 - 08:12:15 PST)
[AMBER] Possible BUG in pmemd.cuda - minimization with igb eq 6
- Marek Maly (Thu Feb 09 2017 - 09:24:22 PST)
- Ross Walker (Thu Feb 09 2017 - 08:43:07 PST)
- Marek Maly (Thu Feb 09 2017 - 07:58:12 PST)
- Ross Walker (Thu Feb 09 2017 - 07:43:18 PST)
- Marek Maly (Thu Feb 09 2017 - 07:09:32 PST)
[AMBER] problem about pressure setting
- David Case (Tue Feb 28 2017 - 05:16:15 PST)
- 吴萌 (Mon Feb 27 2017 - 19:40:24 PST)
[AMBER] Problem using nmropt=1 with CUDA - AMBER 14
- David Case (Thu Feb 16 2017 - 19:34:57 PST)
- Jenner Bonanata (Thu Feb 16 2017 - 09:09:16 PST)
[AMBER] problem with CpHMD
- Michael Shokhen (Tue Feb 21 2017 - 05:31:21 PST)
- Roitberg,Adrian E (Tue Feb 21 2017 - 05:23:58 PST)
- David Case (Tue Feb 21 2017 - 05:22:40 PST)
- Michael Shokhen (Tue Feb 21 2017 - 05:19:07 PST)
- Roitberg,Adrian E (Tue Feb 21 2017 - 04:36:47 PST)
- Michael Shokhen (Tue Feb 21 2017 - 04:03:39 PST)
[AMBER] Problem with mmpbsa
- David Case (Mon Feb 20 2017 - 07:33:18 PST)
- Bill Ross (Mon Feb 20 2017 - 04:46:38 PST)
- Elvis Martis (Mon Feb 20 2017 - 04:15:15 PST)
- Tiffani Rovira (Mon Feb 20 2017 - 04:11:04 PST)
[AMBER] Problems reading in TIP3P parameters
- Daniel Roe (Sun Feb 26 2017 - 10:57:46 PST)
- Geoffrey Gray (Sun Feb 26 2017 - 09:51:33 PST)
[AMBER] problems with heating
- David Case (Sat Feb 25 2017 - 06:33:31 PST)
- Bill Ross (Fri Feb 24 2017 - 02:00:14 PST)
- Bill Ross (Fri Feb 24 2017 - 01:22:23 PST)
- Alicia Merlino (Thu Feb 23 2017 - 20:52:53 PST)
- Bill Ross (Thu Feb 23 2017 - 20:18:23 PST)
- Alicia Merlino (Thu Feb 23 2017 - 20:09:37 PST)
- Alicia Merlino (Thu Feb 23 2017 - 20:05:04 PST)
- Bill Ross (Thu Feb 23 2017 - 19:12:33 PST)
- Alicia Merlino (Thu Feb 23 2017 - 18:23:04 PST)
- Alicia Merlino (Wed Feb 22 2017 - 21:01:14 PST)
- Bill Ross (Wed Feb 22 2017 - 20:38:06 PST)
- Alicia Merlino (Wed Feb 22 2017 - 20:32:36 PST)
- Alicia Merlino (Wed Feb 22 2017 - 20:00:23 PST)
- Alicia Merlino (Wed Feb 22 2017 - 19:30:41 PST)
- Alicia Merlino (Wed Feb 22 2017 - 15:13:10 PST)
- Alicia Merlino (Wed Feb 22 2017 - 14:57:40 PST)
- David Case (Wed Feb 22 2017 - 12:49:35 PST)
- Hai Nguyen (Wed Feb 22 2017 - 11:29:42 PST)
- Alicia Merlino (Wed Feb 22 2017 - 11:24:34 PST)
[AMBER] production error.
- Hai Nguyen (Tue Feb 14 2017 - 10:09:42 PST)
- Saman Yousuf ali (Tue Feb 14 2017 - 09:42:42 PST)
- David Case (Tue Feb 14 2017 - 09:15:36 PST)
- Saman Yousuf ali (Tue Feb 14 2017 - 07:50:26 PST)
- David Case (Tue Feb 14 2017 - 06:15:29 PST)
- Elvis Martis (Mon Feb 13 2017 - 23:04:32 PST)
- Saman Yousuf ali (Mon Feb 13 2017 - 21:37:46 PST)
[AMBER] protocol for simulating a system in NaCl using xleaP module
- zeba firdows (Fri Feb 03 2017 - 03:33:42 PST)
- Elvis Martis (Fri Feb 03 2017 - 03:30:24 PST)
- zeba firdows (Fri Feb 03 2017 - 03:25:58 PST)
- Elvis Martis (Fri Feb 03 2017 - 03:21:14 PST)
- zeba firdows (Thu Feb 02 2017 - 23:27:08 PST)
[AMBER] QM method used for force constants derivation in GAFF2 ?
- Marek Maly (Thu Feb 09 2017 - 18:20:19 PST)
- Karl Kirschner (Mon Feb 06 2017 - 01:48:03 PST)
- Marek Maly (Sat Feb 04 2017 - 19:24:56 PST)
[AMBER] Radical Carbon
- Anna Cebrian Prats (Wed Feb 01 2017 - 06:42:14 PST)
- David Case (Wed Feb 01 2017 - 05:04:07 PST)
[AMBER] Regarding forcefields for Z-DNA
- Jiri Sponer (Sat Feb 04 2017 - 03:13:55 PST)
- Josh Berryman (Wed Feb 01 2017 - 01:38:24 PST)
[AMBER] REMD potential energy fluctuation
- sarah colin (Fri Feb 24 2017 - 03:18:15 PST)
[AMBER] request for input files
- Hannes Loeffler (Mon Feb 27 2017 - 10:43:51 PST)
- Adrian Roitberg (Mon Feb 27 2017 - 10:24:56 PST)
[AMBER] Sander python API problem (?)
- Daniel Roe (Fri Feb 24 2017 - 11:27:43 PST)
- Daniel Roe (Fri Feb 24 2017 - 06:42:38 PST)
- Elisa Pieri (Fri Feb 24 2017 - 06:40:46 PST)
- Hai Nguyen (Fri Feb 24 2017 - 06:38:02 PST)
- Hai Nguyen (Fri Feb 24 2017 - 06:35:20 PST)
- Elisa Pieri (Fri Feb 24 2017 - 06:23:19 PST)
- Elisa Pieri (Fri Feb 24 2017 - 02:24:33 PST)
- Hai Nguyen (Thu Feb 23 2017 - 09:55:53 PST)
- Elisa Pieri (Thu Feb 23 2017 - 08:18:05 PST)
- Nhai (Thu Feb 23 2017 - 08:10:14 PST)
- Elisa Pieri (Thu Feb 23 2017 - 07:54:52 PST)
- Elisa Pieri (Thu Feb 23 2017 - 07:43:05 PST)
- Nhai (Thu Feb 23 2017 - 07:36:37 PST)
- Elisa Pieri (Thu Feb 23 2017 - 07:05:15 PST)
[AMBER] scale part of the system with Parmed
- Qinghua Liao (Thu Feb 23 2017 - 04:42:11 PST)
[AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue
- Elvis Martis (Thu Feb 23 2017 - 08:35:11 PST)
- Nikolay N. Kuzmich (Thu Feb 23 2017 - 06:49:01 PST)
- David Case (Wed Feb 22 2017 - 11:27:21 PST)
- Elvis Martis (Wed Feb 22 2017 - 08:25:20 PST)
- Nikolay N. Kuzmich (Wed Feb 22 2017 - 07:20:16 PST)
- Elvis Martis (Tue Feb 21 2017 - 08:21:23 PST)
- David Case (Tue Feb 21 2017 - 06:32:02 PST)
- Nikolay N. Kuzmich (Tue Feb 21 2017 - 06:03:32 PST)
[AMBER] Should ig value be set explicitly?
- Azade Yazdan Yar (Mon Feb 13 2017 - 08:45:11 PST)
- Adrian Roitberg (Mon Feb 13 2017 - 08:42:18 PST)
- Hai Nguyen (Mon Feb 13 2017 - 08:40:24 PST)
- Azade Yazdan Yar (Mon Feb 13 2017 - 08:17:41 PST)
[AMBER] Simulations with R_OF_GYRATION
- Osman, Roman (Wed Feb 15 2017 - 16:53:12 PST)
- Osman, Roman (Wed Feb 15 2017 - 16:53:15 PST)
- Feng Pan (Wed Feb 15 2017 - 13:56:40 PST)
- Osman, Roman (Wed Feb 15 2017 - 11:34:10 PST)
- Adrian Roitberg (Wed Feb 15 2017 - 11:31:14 PST)
- Osman, Roman (Wed Feb 15 2017 - 11:29:30 PST)
[AMBER] SO4 molecule xleap
- Elvis Martis (Mon Feb 20 2017 - 03:35:02 PST)
- ARMIN HODAEI (Mon Feb 20 2017 - 02:53:06 PST)
[AMBER] STRIP
- Daniel Roe (Fri Feb 24 2017 - 11:40:16 PST)
- Thakur, Abhishek (Fri Feb 24 2017 - 11:36:55 PST)
[AMBER] Thiophosphate paramters - AMBER
- Abhilash J (Thu Feb 02 2017 - 05:41:23 PST)
- Elvis Martis (Wed Feb 01 2017 - 19:53:02 PST)
- Balaji Selvam (Wed Feb 01 2017 - 10:33:12 PST)
[AMBER] This error may be due to faulty Connection atoms when using cationic dummy model
- Qinghua Liao (Thu Feb 23 2017 - 04:11:37 PST)
- JinpengYang (Thu Feb 23 2017 - 03:59:05 PST)
[AMBER] tleap error
- Elvis Martis (Tue Feb 21 2017 - 02:06:14 PST)
- Bill Ross (Mon Feb 20 2017 - 22:53:16 PST)
- Manjula Saravanan (Mon Feb 20 2017 - 22:48:03 PST)
[AMBER] Tleap is making C instaed of Cl
- Thakur, Abhishek (Fri Feb 03 2017 - 06:49:10 PST)
- Daniel Roe (Fri Feb 03 2017 - 05:47:29 PST)
- James Kress (Thu Feb 02 2017 - 19:14:04 PST)
- Thakur, Abhishek (Thu Feb 02 2017 - 16:45:00 PST)
- James Kress (Thu Feb 02 2017 - 16:00:19 PST)
- Thakur, Abhishek (Thu Feb 02 2017 - 14:23:57 PST)
- Thakur, Abhishek (Thu Feb 02 2017 - 14:22:23 PST)
- Thakur, Abhishek (Thu Feb 02 2017 - 13:56:50 PST)
- David Case (Thu Feb 02 2017 - 12:51:31 PST)
- Thakur, Abhishek (Thu Feb 02 2017 - 09:46:30 PST)
- David Case (Thu Feb 02 2017 - 09:37:35 PST)
- Thakur, Abhishek (Thu Feb 02 2017 - 09:09:45 PST)
[AMBER] Two Ph.D. positions in molecular simulations
- Jan Brezovsky (Wed Feb 01 2017 - 13:35:12 PST)
[AMBER] Using CHARMM 36 force field in AMBER
- Brian Radak (Mon Feb 20 2017 - 07:55:56 PST)
[AMBER] VdW parameters in AMBER
- Andreas Gavrielides (Thu Feb 09 2017 - 03:25:25 PST)
- David Case (Wed Feb 08 2017 - 10:28:42 PST)
- Andreas Gavrielides (Wed Feb 08 2017 - 08:48:12 PST)
[AMBER] Velocity file output AMBER16
- Korey M Reid (Tue Feb 14 2017 - 11:39:04 PST)
- David Case (Tue Feb 14 2017 - 06:10:49 PST)
- Elvis Martis (Mon Feb 13 2017 - 20:00:55 PST)
- Korey M Reid (Mon Feb 13 2017 - 13:14:46 PST)
[AMBER] When does cpptraj use information from the original pdb file?
- Daniel Roe (Tue Feb 21 2017 - 06:30:27 PST)
- Markowska (Tue Feb 21 2017 - 05:54:17 PST)
[AMBER] ZAFF LEAP Carbonic Anhydrase II Protein Topology & Coordinate Preparation
- nti.georgetown.edu (Mon Feb 13 2017 - 09:03:49 PST)
- Pengfei Li (Fri Feb 10 2017 - 14:56:56 PST)
- Naiem Issa (Fri Feb 10 2017 - 13:04:53 PST)
- Pengfei Li (Fri Feb 10 2017 - 12:50:57 PST)
- Naiem Issa (Fri Feb 10 2017 - 12:43:53 PST)
[AMBER] 回复： Using CHARMM 36 force field in AMBER
- Chris Neale (Tue Feb 21 2017 - 19:50:02 PST)
- Jason Swails (Tue Feb 21 2017 - 19:25:52 PST)
- Shanghaitech University WuMeng (Tue Feb 21 2017 - 17:56:37 PST)
Failed to calculate entropy with mm_pbsa.pl in AMBER14, with no error informations reported in nmode_com.1.out
- Elvis Martis (Thu Feb 09 2017 - 17:31:08 PST)
- Daniel Roe (Thu Feb 09 2017 - 17:16:32 PST)
- wei (Thu Feb 09 2017 - 15:48:42 PST)
Failed to calculate entropy with mm_pbsa.pl in AMBER14, with no error_informations_reported_in_nmode_com.1.out
- Elvis Martis (Fri Feb 10 2017 - 21:25:07 PST)
Hydrophobic and pi-pi interaction
- chemocev marker (Thu Feb 16 2017 - 08:05:57 PST)
- Thakur, Abhishek (Thu Feb 16 2017 - 05:08:58 PST)

Amber Archive Feb 2017 by subject