Amber Archive Aug 2016 by thread
- [AMBER] EEL energy of QM/MM-GBSA 张姝姝 (Sun Jul 31 2016 - 20:11:42 PDT)
- Re: [AMBER] EEL become ****** in minimization Suguru ASAI (Sun Jul 31 2016 - 21:10:44 PDT)
- Re: [AMBER] Sander bomb: how to create a larger box Ruth Helena Tichauer (Mon Aug 01 2016 - 03:53:51 PDT)
- [AMBER] Use two different force fields in Amber Xiaoliu Zhang (Mon Aug 01 2016 - 07:41:19 PDT)
- [AMBER] subject: parametrization of Force field DOCENTE ANTISTIO ANIBAL ALVIS AMADOR (Mon Aug 01 2016 - 07:50:08 PDT)
- [AMBER] EVB calculations of proton transfer David A Case (Mon Aug 01 2016 - 07:52:43 PDT)
- [AMBER] tinker_to_amber error Xiaoliu Zhang (Mon Aug 01 2016 - 08:52:17 PDT)
- [AMBER] default value (inp= 0,1,2)? MMPBSA Thakur, Abhishek (Mon Aug 01 2016 - 09:35:16 PDT)
- Re: [AMBER] hydrogen bond occupancy plot cpptraj Daniel Roe (Mon Aug 01 2016 - 10:23:57 PDT)
- Re: [AMBER] Calculating Salt bridge interactions- Protein and RNA Daniel Roe (Mon Aug 01 2016 - 10:26:14 PDT)
- Re: [AMBER] Difference of two trajectories Daniel Roe (Mon Aug 01 2016 - 10:27:33 PDT)
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice (Mon Aug 01 2016 - 12:06:53 PDT)
- [AMBER] which forcefield it is? Albert (Mon Aug 01 2016 - 23:38:43 PDT)
- Re: [AMBER] InVacuoWithDielc JAIME RUBIO MARTINEZ (Tue Aug 02 2016 - 00:32:58 PDT)
- [AMBER] HBond command Sidhu, Khushwant (Dr.) (Tue Aug 02 2016 - 05:50:08 PDT)
- [AMBER] interaction entropy instead of normal mode analysis diaby (Tue Aug 02 2016 - 06:57:10 PDT)
- Re: [AMBER] Energy overflow in MD with distance restraint under PBC (aMD problem?) Stephan Schott (Tue Aug 02 2016 - 07:00:29 PDT)
- [AMBER] correlated dihedral force constant Chi Jin (Tue Aug 02 2016 - 12:46:23 PDT)
- [AMBER] EM in vacuum Dmitry Suplatov (Tue Aug 02 2016 - 13:52:17 PDT)
- [AMBER] running RISM/MD on multi processors Jingyi Yan (Tue Aug 02 2016 - 14:26:16 PDT)
- [AMBER] the phosphoric acid group is deformed 乔艳 (Tue Aug 02 2016 - 16:40:30 PDT)
- [AMBER] the end phosphoric acid group is deformed during simulation rain (Tue Aug 02 2016 - 17:12:34 PDT)
- [AMBER] parmchk vs parmchk2 Andrew.Warden.csiro.au (Tue Aug 02 2016 - 21:53:09 PDT)
- [AMBER] Amber´14 Solvent box simulation, something went wrong!! Stregone (Wed Aug 03 2016 - 06:43:18 PDT)
- [AMBER] Cyana3.97 to Amber15 pdb conversion Erik Davis (Wed Aug 03 2016 - 08:09:35 PDT)
- [AMBER] gbsa parameter Thomas Evangelidis (Wed Aug 03 2016 - 08:54:11 PDT)
- [AMBER] save Hessian nmode mmpbsa Bruno Falcone (Wed Aug 03 2016 - 09:51:23 PDT)
- [AMBER] Generate Polymer parameters konda003 . (Wed Aug 03 2016 - 12:58:24 PDT)
- [AMBER] 180 degrees of angle in AMBER 10 Pengzhi Zhang (Wed Aug 03 2016 - 13:07:26 PDT)
- [AMBER] Getting free energy (difference) from GPU simulations yunshi11 . (Wed Aug 03 2016 - 16:18:05 PDT)
- [AMBER] error in runing mdout_analyzer.py nida baig (Wed Aug 03 2016 - 21:10:04 PDT)
- [AMBER] error running production with restraint. Saman Yousuf ali (Wed Aug 03 2016 - 22:16:51 PDT)
- [AMBER] solvate hexagonal box Neha Gandhi (Wed Aug 03 2016 - 22:29:52 PDT)
- [AMBER] Is there a way to disable electrostatic solute-solvent interactions in PMEMD? Plotnikov, Nikolay (Thu Aug 04 2016 - 08:27:25 PDT)
- [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht (Thu Aug 04 2016 - 10:59:10 PDT)
- [AMBER] unreadable crd files macc_200 (Thu Aug 04 2016 - 14:47:48 PDT)
- [AMBER] MMPBSA.py TrajError: Could not find number of frames in .mdcrd maryam azimzadehirani (Thu Aug 04 2016 - 20:52:07 PDT)
- [AMBER] amber16/test/qmmm_DFTB Markus Kaukonen (Thu Aug 04 2016 - 23:13:12 PDT)
- [AMBER] QMMM MD, Simulation does not start Stregone (Fri Aug 05 2016 - 06:29:59 PDT)
- [AMBER] Cpptraj-PCA Warning Ilkow, Veronica (Fri Aug 05 2016 - 07:15:50 PDT)
- [AMBER] Amber14 FEW for 3 trajectory free energy JoAnne Babula (Fri Aug 05 2016 - 07:32:22 PDT)
- [AMBER] Implicit solvent in pmemd.cuda Chitrak Gupta (Fri Aug 05 2016 - 08:54:58 PDT)
- [AMBER] Error with nmode calculations Praneeth Bommisetti (Fri Aug 05 2016 - 11:10:32 PDT)
- [AMBER] restraining mean square displacements Irem Altan (Fri Aug 05 2016 - 12:52:35 PDT)
- [AMBER] box of polar molecules using amoeba force field Xiaoliu Zhang (Fri Aug 05 2016 - 14:32:46 PDT)
- [AMBER] Extend of manual modulation-Connecting two molecules methodology Kostas Bourandas (Sat Aug 06 2016 - 13:32:44 PDT)
- [AMBER] How to fix the wall of the water box in amber Ming Tang (Sat Aug 06 2016 - 18:17:18 PDT)
- [AMBER] copy charges using Python API Thomas Evangelidis (Sun Aug 07 2016 - 04:28:38 PDT)
- Re: [AMBER] SMD simulation bharat gupta (Sun Aug 07 2016 - 22:44:08 PDT)
- [AMBER] intel MPI failed Albert (Mon Aug 08 2016 - 06:40:54 PDT)
- [AMBER] reweighting scheme Thakur, Abhishek (Mon Aug 08 2016 - 12:02:00 PDT)
- [AMBER] phi-psi distribution Thakur, Abhishek (Mon Aug 08 2016 - 13:54:24 PDT)
- [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water Corum, Katharine W (Mon Aug 08 2016 - 14:33:12 PDT)
- [AMBER] query regarding restraint on specific residues. Saman Yousuf ali (Tue Aug 09 2016 - 00:00:57 PDT)
- [AMBER] {AMBER} installation on mac osx 10.11.6 hanging when configuring NetCDF mirko hennig (Tue Aug 09 2016 - 00:53:23 PDT)
- [AMBER] Off , mol2 and frcmod files Christopher Jesudason (Tue Aug 09 2016 - 04:40:25 PDT)
- [AMBER] for what kind of post simulation analysis I need to do reweighing? Thakur, Abhishek (Tue Aug 09 2016 - 08:01:27 PDT)
- [AMBER] simultaneous use of ibelly=1 and ntr=1 Saman Yousuf ali (Tue Aug 09 2016 - 08:54:47 PDT)
- [AMBER] Converting rst to pdb Corum, Katharine W (Tue Aug 09 2016 - 14:01:58 PDT)
- [AMBER] Amber 14.13 pmemd.cuda: Error: invalid configuration argument launching kernel kPMEReduceChargeGridBuffer William Lees (Wed Aug 10 2016 - 02:02:59 PDT)
- [AMBER] does AMBER already have Pt parameters for modeling cisplatin like compounds? Vaibhav Dixit (Wed Aug 10 2016 - 04:49:05 PDT)
- [AMBER] 3 trajectory MMPBSA free energy calculation JoAnne Babula (Wed Aug 10 2016 - 07:47:45 PDT)
- [AMBER] Regarding antechamber command Error Vishal Nemaysh (Wed Aug 10 2016 - 08:47:05 PDT)
- [AMBER] paper describing the ff15ipq protein force field is now available David A Case (Wed Aug 10 2016 - 11:11:08 PDT)
- [AMBER] antechamber cannot match patching atoms of amino acid Chitrak Gupta (Wed Aug 10 2016 - 15:26:24 PDT)
- [AMBER] GPU MPI failed Albert (Thu Aug 11 2016 - 01:37:52 PDT)
- [AMBER] Amber16 installation error. Abhilash J (Thu Aug 11 2016 - 07:55:00 PDT)
- [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula (Thu Aug 11 2016 - 08:21:11 PDT)
- [AMBER] secondary structure graph vs Time Parviz Seifpanahi Shabane (Thu Aug 11 2016 - 09:03:01 PDT)
- [AMBER] Running tleap with old prmtop Taylor Quinn (Thu Aug 11 2016 - 10:13:09 PDT)
- [AMBER] GPU peer support disabled Hirdesh Kumar (Thu Aug 11 2016 - 13:53:22 PDT)
- [AMBER] LINMIN FAILURE on large protein minimization with GB and explicit SUNHEE CHO (Thu Aug 11 2016 - 18:25:19 PDT)
- Re: [AMBER] Amber16 Parallel CUDA Tests Steven Ford (Thu Aug 11 2016 - 19:54:15 PDT)
- [AMBER] not sure if this is an ERROR in installation please suggest Vaibhav Dixit (Thu Aug 11 2016 - 20:44:07 PDT)
- [AMBER] amber pdb > 100,000 atoms Neha Gandhi (Fri Aug 12 2016 - 00:53:28 PDT)
- [AMBER] modeling flexible loops in protein-DNA complexes Vlad Cojocaru (Fri Aug 12 2016 - 01:43:23 PDT)
- [AMBER] Optimal force constant for AMBER Stregone (Fri Aug 12 2016 - 06:29:15 PDT)
- [AMBER] job suspended Albert (Fri Aug 12 2016 - 06:33:22 PDT)
- [AMBER] MASK with distance in AMBER. Parviz Seifpanahi Shabane (Fri Aug 12 2016 - 08:48:32 PDT)
- [AMBER] umbrella sampling restraining both angle and distance Thakur, Abhishek (Fri Aug 12 2016 - 09:50:11 PDT)
- [AMBER] cpptraj issues Thomas Pochapsky (Fri Aug 12 2016 - 09:52:19 PDT)
- [AMBER] Two ion problem with mcpb.py Abhilash J (Fri Aug 12 2016 - 10:11:55 PDT)
- [AMBER] Amber B5 tutorial Chitrak Gupta (Fri Aug 12 2016 - 11:10:05 PDT)
- [AMBER] Accelerated MD -- cudaMemcpy error Dmitry Suplatov (Fri Aug 12 2016 - 13:53:07 PDT)
- [AMBER] Question of Parameter Defaults Robert Molt (Fri Aug 12 2016 - 18:00:57 PDT)
- [AMBER] job failed Albert (Sat Aug 13 2016 - 23:37:26 PDT)
- [AMBER] error in sander and sander.mpi running leila karami (Sun Aug 14 2016 - 04:11:11 PDT)
- [AMBER] error in sander and sander.mpi running leila karami (Sun Aug 14 2016 - 05:24:31 PDT)
- [AMBER] solid surface simulation in amber Neha Gandhi (Sun Aug 14 2016 - 23:59:57 PDT)
- [AMBER] parmchk2 issue Hannes Loeffler (Mon Aug 15 2016 - 08:06:38 PDT)
- [AMBER] QM/MM stops at step 2114 Corum, Katharine W (Mon Aug 15 2016 - 08:08:25 PDT)
- [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan mirko hennig (Mon Aug 15 2016 - 09:26:56 PDT)
- [AMBER] CHARM force field Chi Jin (Mon Aug 15 2016 - 13:48:12 PDT)
- [AMBER] bellymask option. Saman Yousuf ali (Mon Aug 15 2016 - 19:24:05 PDT)
- [AMBER] lipid simulation with Lipid14 FF failed Albert (Tue Aug 16 2016 - 03:00:50 PDT)
- [AMBER] Water flexibility in QM/MM simulation Ruth Helena Tichauer (Tue Aug 16 2016 - 09:27:14 PDT)
- [AMBER] Restarting a crushed run DmitryASuplatov (Tue Aug 16 2016 - 09:43:44 PDT)
- [AMBER] Regarding the free energy calculation Sivanandam M (Tue Aug 16 2016 - 11:00:06 PDT)
- [AMBER] Combining single structure NMR pdb files into an ensemble. Erik Davis (Tue Aug 16 2016 - 13:38:05 PDT)
- [AMBER] about lipids retrain Albert (Wed Aug 17 2016 - 02:45:19 PDT)
- [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Cecilia Lindgren (Wed Aug 17 2016 - 05:56:24 PDT)
- [AMBER] Is there any CG martini parameter for K+? li he (Wed Aug 17 2016 - 11:18:34 PDT)
- [AMBER] Problem when visualizing bonds in VMD Xiaoliu Zhang (Wed Aug 17 2016 - 12:40:22 PDT)
- [AMBER] QM region has an odd number of electrons Corum, Katharine W (Wed Aug 17 2016 - 14:22:53 PDT)
- [AMBER] RMSd Wong Li Zhe (Wed Aug 17 2016 - 21:08:05 PDT)
- [AMBER] LEaP and PARMSETs Aronica, Pietro (Thu Aug 18 2016 - 01:49:50 PDT)
- [AMBER] a bug in leaprc.gaff2 file Ye Mei (Thu Aug 18 2016 - 02:21:16 PDT)
- [AMBER] Problem in charge generation through antechamber ATUL KUMAR (Thu Aug 18 2016 - 11:53:45 PDT)
- [AMBER] percentages of protein secondary structure. Saman Yousuf ali (Thu Aug 18 2016 - 21:17:59 PDT)
- [AMBER] Does Scaled MD require NVT ensemble? Harshavardhan Khare (Thu Aug 18 2016 - 23:20:40 PDT)
- [AMBER] Temperature Shoot-up in TMD Aravind Ravichandran (Fri Aug 19 2016 - 00:26:24 PDT)
- [AMBER] What cutoff you use in Amber simulations? DmitryASuplatov (Fri Aug 19 2016 - 04:35:40 PDT)
- [AMBER] Tutorial B5 - Loading CRO from ccif file Alfredo Quevedo (Fri Aug 19 2016 - 07:26:42 PDT)
- [AMBER] concerns on membrane protein restrain Albert (Fri Aug 19 2016 - 11:39:35 PDT)
- [AMBER] WHAM analysis Thakur, Abhishek (Fri Aug 19 2016 - 14:55:16 PDT)
- [AMBER] minimum restraint_wt. Saman Yousuf ali (Sun Aug 21 2016 - 00:05:43 PDT)
- [AMBER] Frac in cpptraj hydrogen bond command. Saman Yousuf ali (Sun Aug 21 2016 - 05:25:42 PDT)
- [AMBER] Adaptively Biased MD Simulations of type "distance" using "FLOODING" Emmanuel (Mon Aug 22 2016 - 03:32:05 PDT)
- [AMBER] Sigma and epsilon vdw parameters Neha Gandhi (Mon Aug 22 2016 - 15:28:44 PDT)
- [AMBER] Output Files Wong Li Zhe (Mon Aug 22 2016 - 18:03:36 PDT)
- [AMBER] Simulation Time Wong Li Zhe (Mon Aug 22 2016 - 22:00:03 PDT)
- [AMBER] Alanine scan of nonnatural amino acid Aronica, Pietro (Tue Aug 23 2016 - 02:21:37 PDT)
- [AMBER] Copper +1 and membrane with LJ 12-6-4 potential Stephan Schott (Tue Aug 23 2016 - 07:37:52 PDT)
- [AMBER] Problem with atommap function in cpptraj (v16) Samuel Bowerman (Tue Aug 23 2016 - 12:23:56 PDT)
- [AMBER] Generating parameter and topology files for a protein with multiple Zinc ions Aditya Padhi (Tue Aug 23 2016 - 18:00:15 PDT)
- [AMBER] Checking modeling after MCPB and unable to fix atom order using cpptraj Andrew Schaub (Tue Aug 23 2016 - 22:15:58 PDT)
- [AMBER] Generating topology and parameter file for a peptide pratibha sharma (Tue Aug 23 2016 - 23:34:57 PDT)
- [AMBER] 22.1.6.1. Free Energy using linear scaling 22.1.6.2.Absolute free energy using soft core, Markus Kaukonen (Wed Aug 24 2016 - 01:01:45 PDT)
- [AMBER] cpptraj on pH-REMD Elisa Pieri (Wed Aug 24 2016 - 04:19:10 PDT)
- [AMBER] Regarding hbond bridgeout Indrajit Deb (Wed Aug 24 2016 - 09:04:17 PDT)
- [AMBER] Issues compiling Amber with CUDA support Sivy, Shawn (Wed Aug 24 2016 - 11:47:10 PDT)
- [AMBER] SEP parameter with ff15ipq vadiraj kurdekar (Thu Aug 25 2016 - 00:08:31 PDT)
- [AMBER] Problem with rst7 Elisa Pieri (Thu Aug 25 2016 - 02:12:46 PDT)
- [AMBER] Fw: Problems to calculate frequencies Stregone (Thu Aug 25 2016 - 03:14:42 PDT)
- [AMBER] output of MMPBSA.py Markus Kaukonen (Thu Aug 25 2016 - 03:43:20 PDT)
- [AMBER] MMPBSA.py CalcError on ligand contribution only Leandro Bortot (Thu Aug 25 2016 - 07:43:11 PDT)
- [AMBER] problem upon optimization giulia palermo (Thu Aug 25 2016 - 08:12:39 PDT)
- [AMBER] Checking AmberTools16 installation Bence Hégely (Thu Aug 25 2016 - 11:53:11 PDT)
- [AMBER] repair mdcrd? Bill Ross (Thu Aug 25 2016 - 13:26:01 PDT)
- [AMBER] begin time read from input coords Hannes Loeffler (Fri Aug 26 2016 - 01:10:09 PDT)
- [AMBER] Multihist in watershell command Damiano Spadoni (Fri Aug 26 2016 - 05:26:24 PDT)
- [AMBER] (no subject) Amrullah13 (Sat Aug 27 2016 - 18:51:50 PDT)
- [AMBER] autoimage bug? Filip Persson (Mon Aug 29 2016 - 05:36:24 PDT)
- [AMBER] autocorr of hydrogen bonds Osman, Roman (Mon Aug 29 2016 - 06:05:06 PDT)
- [AMBER] errors in doing TI tutorial calculation 张姝姝 (Mon Aug 29 2016 - 07:26:56 PDT)
- [AMBER] restraint does not work in mininmization Michael Shokhen (Tue Aug 30 2016 - 00:48:54 PDT)
- [AMBER] frozen geometry setting? Michael Shokhen (Tue Aug 30 2016 - 07:32:09 PDT)
- [AMBER] Parameters for modified nucleosides Tomek Wlodarski (Tue Aug 30 2016 - 10:34:09 PDT)
- [AMBER] lowering the temperature Thomas Evangelidis (Tue Aug 30 2016 - 16:51:40 PDT)
- [AMBER] change the atom charge in a restart simulations windy (Wed Aug 31 2016 - 01:49:25 PDT)
- [AMBER] changing atom type Jacopo Sgrignani (Wed Aug 31 2016 - 08:16:37 PDT)
- [AMBER] QM/MM energy units? Corum, Katharine W (Wed Aug 31 2016 - 08:52:45 PDT)
- [AMBER] File redirection commands with targeted MD Sonia Ziada (Wed Aug 31 2016 - 09:10:52 PDT)
- [AMBER] Amber Force Fields amir sadeghi (Wed Aug 31 2016 - 12:33:48 PDT)
- [AMBER] Regarding the use of sed command to replace water Budhathoki, Dipesh (Wed Aug 31 2016 - 12:52:37 PDT)
- Last message date: Wed Aug 31 2016 - 18:00:02 PDT
- Archived on: Wed Dec 25 2024 - 05:55:24 PST
