Amber Archive Aug 2015 by thread
- [AMBER] cudaMemcpy GpuBuffer::Download failed - hardware or software? Eugene Radchenko (Sat Aug 01 2015 - 13:30:14 PDT)
- [AMBER] algorithm for clustering solvent molecules? Jose Borreguero (Sat Aug 01 2015 - 18:23:42 PDT)
- [AMBER] Implicit solvent simulation is unexpectedly slow 浅井 賢 (Sun Aug 02 2015 - 01:21:43 PDT)
- [AMBER] Does the "contacts" command of cpptraj implement imaging? Jose Borreguero (Sun Aug 02 2015 - 15:47:19 PDT)
- [AMBER] PCA: generate histogram George Tzotzos (Mon Aug 03 2015 - 03:46:55 PDT)
- Re: [AMBER] Antechamber for boronic acid derivatives? David A Case (Mon Aug 03 2015 - 04:56:36 PDT)
- [AMBER] FW: PMEMD: Warning: ieee_inexact is signaling Khabiri, Morteza (Mon Aug 03 2015 - 06:26:01 PDT)
- [AMBER] Installation of AmberTools 15. Overriding earlier installation George Tzotzos (Mon Aug 03 2015 - 12:26:25 PDT)
- Re: [AMBER] PMEMD: Warning: ieee_inexact is signaling Khabiri, Morteza (Mon Aug 03 2015 - 12:40:14 PDT)
- [AMBER] MM-PBSA free energy calculation with keeping x-ray water bharat lakhani (Mon Aug 03 2015 - 12:45:26 PDT)
- Re: [AMBER] MCPB.py mismatch error Eleftherios A P Lambros (Mon Aug 03 2015 - 13:39:05 PDT)
- [AMBER] MM-PBSA atom types bharat lakhani (Mon Aug 03 2015 - 15:24:53 PDT)
- [AMBER] Bad Atom type during running MMPBSA with cobalt metal ion MOHD HOMAIDUR RAHMAN (Mon Aug 03 2015 - 23:23:36 PDT)
- [AMBER] Trying to perform a heating MD in increments Amber mail (Tue Aug 04 2015 - 01:39:02 PDT)
- [AMBER] MMPBSA.py problem Debodyuti Dutta (Tue Aug 04 2015 - 03:16:45 PDT)
- [AMBER] How to construct the Ala3 peptide shown in this picture? lipengfei_mail (Tue Aug 04 2015 - 05:12:38 PDT)
- [AMBER] ired analysis: No modes data specified Kris Feher (Tue Aug 04 2015 - 05:23:53 PDT)
- [AMBER] PCA analysis anu chandra (Tue Aug 04 2015 - 15:55:05 PDT)
- [AMBER] NaN with pmemd.cuda Joseph Baker (Tue Aug 04 2015 - 21:43:22 PDT)
- [AMBER] Regarding DNA forcefield in Amber14 Pragya Priyadarshini (Wed Aug 05 2015 - 00:35:34 PDT)
- [AMBER] PCA: comparing PCs from different trajectories George Tzotzos (Wed Aug 05 2015 - 01:24:45 PDT)
- [AMBER] MMPBSA_Ras-Raf complex tutorial Ruchika Bhat (Wed Aug 05 2015 - 06:48:17 PDT)
- [AMBER] antechamber error Lara rajam (Wed Aug 05 2015 - 07:27:08 PDT)
- [AMBER] .mdcrd to .trr conversion problem Vishal Nemaysh (Wed Aug 05 2015 - 08:41:51 PDT)
- [AMBER] [cpptraj] Kullback Leibler Divergence cutoff choice Eiros Zamora, Juan (Wed Aug 05 2015 - 09:01:18 PDT)
- [AMBER] issue with 4 fs hydrogen mass repartitioning taking more time than a standard 2 fs simulation in AMBER14 George Green (Wed Aug 05 2015 - 16:28:31 PDT)
- [AMBER] Thermodynamic integration goes wrong in lambda =0 while lambda = 1 is ok!! Khabiri, Morteza (Wed Aug 05 2015 - 18:34:39 PDT)
- [AMBER] RED Server for Altered Amino Acid Edward Kalkreuter (Wed Aug 05 2015 - 19:56:11 PDT)
- [AMBER] large .mdcrd splitting Vishal Nemaysh (Thu Aug 06 2015 - 00:49:02 PDT)
- [AMBER] could not open mdcrd file Vahid Kshani (Thu Aug 06 2015 - 04:22:21 PDT)
- [AMBER] Problem with cpptraj autoimage command Karolina Markowska (Thu Aug 06 2015 - 04:35:59 PDT)
- [AMBER] SPAM Sarah Graham (Thu Aug 06 2015 - 11:06:23 PDT)
- [AMBER] "mask" command failure Ucisik, Melek Nihan (Thu Aug 06 2015 - 14:26:40 PDT)
- [AMBER] parmch2 versus parmchk CHAMI F. (Fri Aug 07 2015 - 06:00:23 PDT)
- [AMBER] awards applications open for ACS Division of Computers in Chemistry Carlos Simmerling (Fri Aug 07 2015 - 08:33:37 PDT)
- [AMBER] MMPBSA error using pbsa2 shenna shearin (Fri Aug 07 2015 - 17:33:56 PDT)
- [AMBER] Automated restart Eugene Radchenko (Sat Aug 08 2015 - 03:40:50 PDT)
- [AMBER] cpptraj - RMSD Amber mail (Sat Aug 08 2015 - 23:51:02 PDT)
- [AMBER] cpptraj gist: Eww energies Thomas Fox (Mon Aug 10 2015 - 02:49:21 PDT)
- [AMBER] mmpbsa.py: Error George Tzotzos (Mon Aug 10 2015 - 09:49:29 PDT)
- [AMBER] FW: Regarding AMBER 14 praSanna kuMar naYak (Tue Aug 11 2015 - 01:47:38 PDT)
- [AMBER] FW: Regarding AMBER14 Error praSanna kuMar naYak (Tue Aug 11 2015 - 01:47:52 PDT)
- [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Sangita Kachhap (Tue Aug 11 2015 - 03:05:20 PDT)
- [AMBER] AMBER 14 installation Problem Himansu (Tue Aug 11 2015 - 03:23:45 PDT)
- [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Amber mail (Tue Aug 11 2015 - 10:18:16 PDT)
- [AMBER] using chamber to convert psf to prmtop KK R (Tue Aug 11 2015 - 13:08:42 PDT)
- [AMBER] Macromolecular crowding force-field and parameters richa anand (Tue Aug 11 2015 - 20:55:40 PDT)
- [AMBER] acetylate and ammoniate mohammad r (Wed Aug 12 2015 - 05:23:39 PDT)
- [AMBER] Warning: ieee_inexact is signaling PMEMD Terminated Abnormally! Khabiri, Morteza (Wed Aug 12 2015 - 06:36:57 PDT)
- [AMBER] cpptraj frames clustering limit Gaurao Dhoke (Wed Aug 12 2015 - 06:46:07 PDT)
- [AMBER] GIST vs. 3D-RISM Thomas Fox (Wed Aug 12 2015 - 08:36:45 PDT)
- [AMBER] cg in GAFF: amb2gmx.pl vs virtualchemistry - LJ well depth Sharapa (Wed Aug 12 2015 - 15:01:40 PDT)
- [AMBER] amber14 gpu webpage lists cuda 7.0 as supported Dow Hurst (Wed Aug 12 2015 - 18:53:11 PDT)
- [AMBER] [Solved] amber14 gpu webpage lists cuda 7.0 as supported Dow Hurst (Wed Aug 12 2015 - 18:59:31 PDT)
- [AMBER] Force-field and parameters richa anand (Wed Aug 12 2015 - 21:32:06 PDT)
- [AMBER] pH-REMD theory whb (Wed Aug 12 2015 - 23:58:47 PDT)
- [AMBER] MMPBSA.py error Urszula Uciechowska (Thu Aug 13 2015 - 03:59:19 PDT)
- [AMBER] Imaging and connectivity error Harmeet Kaur (Thu Aug 13 2015 - 04:27:24 PDT)
- [AMBER] dynlmb and TI Khabiri, Morteza (Thu Aug 13 2015 - 11:36:11 PDT)
- [AMBER] ImportError: No module named mcpb.gene_model_files Marcelo Andrade Chagas (Thu Aug 13 2015 - 12:14:22 PDT)
- [AMBER] Job submission script for SGE Himansu (Thu Aug 13 2015 - 16:50:59 PDT)
- [AMBER] The protein is Leaving the water box! Amber mail (Thu Aug 13 2015 - 17:36:59 PDT)
- [AMBER] help in rdf Robin Jain (Fri Aug 14 2015 - 00:59:12 PDT)
- [AMBER] the better box size Investigador Química (Fri Aug 14 2015 - 10:45:56 PDT)
- [AMBER] RMSD and average value of interatomic distance? Michael Shokhen (Sat Aug 15 2015 - 00:30:26 PDT)
- Re: [AMBER] AMBER Digest, Vol 1311, Issue 1 Robin Jain (Sat Aug 15 2015 - 01:58:47 PDT)
- [AMBER] About the QMMM simulation with LIO software Yeng-Tseng Wang (Sat Aug 15 2015 - 09:58:47 PDT)
- [AMBER] A query about MMPBSA.py calcualtion anu chandra (Sun Aug 16 2015 - 06:45:50 PDT)
- [AMBER] ****** in results? Chinh Su Tran To (Sun Aug 16 2015 - 23:51:48 PDT)
- [AMBER] Help needed regarding simulating Lipopolysaccharide Mrinda Jones (Mon Aug 17 2015 - 03:41:39 PDT)
- [AMBER] STOP PMEMD Terminated Abnormally! Pragya Priyadarshini (Mon Aug 17 2015 - 04:14:11 PDT)
- [AMBER] saveamberparm mohammad r (Mon Aug 17 2015 - 07:14:26 PDT)
- [AMBER] Big potential difference between conformation in MD simulation and optimized conformation in Gaussian. Eg eh (Mon Aug 17 2015 - 12:08:44 PDT)
- [AMBER] calculation of rmsd with cpptraj Krantzman, Kristin D (Mon Aug 17 2015 - 12:53:05 PDT)
- [AMBER] cpptraj cluster in MPI Lara rajam (Mon Aug 17 2015 - 19:43:09 PDT)
- [AMBER] Immediate PhD Opening In Computational Structural Biology Of Membrane Proteins Marawan Hussien (Mon Aug 17 2015 - 20:25:18 PDT)
- [AMBER] Immediate Postdoctoral Position Opening In Computational Chemistry And Computer-Aided Drug Design (CADD) Marawan Hussien (Mon Aug 17 2015 - 20:26:39 PDT)
- [AMBER] acpype mohammad r (Mon Aug 17 2015 - 23:58:54 PDT)
- [AMBER] acpype mohammad r (Tue Aug 18 2015 - 01:17:59 PDT)
- [AMBER] ancpype problem mohammad r (Tue Aug 18 2015 - 02:00:36 PDT)
- [AMBER] Total interaction energy between monomeric units of a dimer anu chandra (Tue Aug 18 2015 - 04:55:46 PDT)
- [AMBER] converting amber files mohammad r (Tue Aug 18 2015 - 05:12:49 PDT)
- [AMBER] NPT equilibration failed Albert (Tue Aug 18 2015 - 05:58:56 PDT)
- [AMBER] hpc error Damiano Spadoni (Tue Aug 18 2015 - 06:43:23 PDT)
- [AMBER] cpptraj RMSD stats George Tzotzos (Tue Aug 18 2015 - 06:43:52 PDT)
- [AMBER] cpptraj perress RMSD George Tzotzos (Tue Aug 18 2015 - 07:47:36 PDT)
- [AMBER] upgrading to AT15 (from AT14) Massimiliano Porrini (Tue Aug 18 2015 - 09:47:00 PDT)
- [AMBER] adding NaCl mohammad r (Tue Aug 18 2015 - 21:32:47 PDT)
- [AMBER] adding NaCl mohammad r (Tue Aug 18 2015 - 22:44:23 PDT)
- [AMBER] CL topology Albert (Wed Aug 19 2015 - 00:04:44 PDT)
- [AMBER] adding NaCl mohammad r (Wed Aug 19 2015 - 00:25:07 PDT)
- [AMBER] RESP fitting Mahmood Jasim (Wed Aug 19 2015 - 05:46:21 PDT)
- Re: [AMBER] the better box size for calculating host-guest interaction energies Investigador Química (Wed Aug 19 2015 - 07:43:41 PDT)
- [AMBER] xleap numbering in residues Lara rajam (Wed Aug 19 2015 - 18:32:00 PDT)
- [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ anu chandra (Thu Aug 20 2015 - 09:35:31 PDT)
- [AMBER] Problem with using the 12-6-4 LJ-Type Nonbonded Model in a an RNA-Mg system Kasprzak, Wojciech (NIH/NCI) [C] (Thu Aug 20 2015 - 13:08:09 PDT)
- [AMBER] Using MMPBSA.py with CHARMM force field Ara Abramyan (Thu Aug 20 2015 - 13:43:11 PDT)
- [AMBER] hydrogen mass repartitioning visualization in chimera George Green (Thu Aug 20 2015 - 16:49:14 PDT)
- [AMBER] Autoimage Warning Brittany Boykin (Fri Aug 21 2015 - 08:10:12 PDT)
- [AMBER] closest command in cpptraj Joseph Baker (Fri Aug 21 2015 - 12:31:26 PDT)
- [AMBER] help in density equilibration Robin Jain (Fri Aug 21 2015 - 22:30:39 PDT)
- [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces Parker de Waal (Sat Aug 22 2015 - 13:58:21 PDT)
- [AMBER] adding lipid mohammad r (Sun Aug 23 2015 - 06:41:32 PDT)
- [AMBER] how to add lipid mohammad r (Sun Aug 23 2015 - 06:47:36 PDT)
- [AMBER] how to add lipid mohammad roostaie (Sun Aug 23 2015 - 07:08:02 PDT)
- [AMBER] tleap ask for bond to zinc ion Jorgen Simonsen (Sun Aug 23 2015 - 08:49:01 PDT)
- [AMBER] help in density equilibration Robin Jain (Sun Aug 23 2015 - 21:00:17 PDT)
- [AMBER] Regarding No of Hydrogen bonds (vs) Residue wise Garisekurthi Satheesh (Sun Aug 23 2015 - 21:15:03 PDT)
- [AMBER] AMBER Autoimage Warning Brittany Boykin (Mon Aug 24 2015 - 09:42:04 PDT)
- [AMBER] ImportError: No module named scipy.optimize Sushi Shilpa (Mon Aug 24 2015 - 21:07:25 PDT)
- [AMBER] how to neutralized my system with Na+ ions Martina Devi (Mon Aug 24 2015 - 23:53:54 PDT)
- [AMBER] Regarding printing of trajectory MOHD HOMAIDUR RAHMAN (Tue Aug 25 2015 - 00:11:55 PDT)
- [AMBER] mismatch base pair from nab Martina Devi (Tue Aug 25 2015 - 04:49:01 PDT)
- [AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids anilkumarsahoo.physics.iisc.ernet.in (Tue Aug 25 2015 - 04:29:38 PDT)
- [AMBER] Non-equilibrium pulling with plane-point restraints Jacob Monroe (Tue Aug 25 2015 - 10:45:22 PDT)
- [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein Wenyu Qian (Tue Aug 25 2015 - 15:04:08 PDT)
- [AMBER] cpin error Arjun Sharma (Tue Aug 25 2015 - 16:45:04 PDT)
- [AMBER] Does it mean the card is damaged? Karolina Markowska (Thu Aug 27 2015 - 01:40:19 PDT)
- [AMBER] Charge-dependent exchange-dispersion corrections Lucas A. Defelipe (Thu Aug 27 2015 - 07:46:23 PDT)
- [AMBER] Molsurf: some questions on usage George Tzotzos (Thu Aug 27 2015 - 08:05:44 PDT)
- Re: [AMBER] Cpin error Arjun Sharma (Thu Aug 27 2015 - 08:31:18 PDT)
- [AMBER] Looking for suggestion for analysis Mohd Farid Ismail (Thu Aug 27 2015 - 19:42:17 PDT)
- [AMBER] Confusion in running QM/MMGBSA MOHD HOMAIDUR RAHMAN (Fri Aug 28 2015 - 12:08:49 PDT)
- [AMBER] How do I study the dimerisation energy (i.e. energy required to form a dimer from two monomeric units) using AMBER? Suchetana Gupta (Sat Aug 29 2015 - 00:15:11 PDT)
- [AMBER] Segmentation Fault with pmemd Ziheng Wang (Sat Aug 29 2015 - 01:02:03 PDT)
- [AMBER] cyclic peptides Lara rajam (Sun Aug 30 2015 - 17:26:27 PDT)
- [AMBER] job submission in RED Martina Devi (Mon Aug 31 2015 - 03:34:40 PDT)
- [AMBER] Thermodynamic integration and segmentation fault Khabiri, Morteza (Mon Aug 31 2015 - 06:40:15 PDT)
- [AMBER] Draw a cube around the molecules Iqbal, Muhammad Sajid (Mon Aug 31 2015 - 11:56:19 PDT)
- Last message date: Mon Aug 31 2015 - 17:00:03 PDT
- Archived on: Mon Dec 02 2024 - 05:55:13 PST
