Amber Archive Nov 2014 by thread
- [AMBER] Calculating Normalised electron density for DOPC. Him Shweta (Sat Nov 01 2014 - 06:10:58 PDT)
- Re: [AMBER] [q4md-fft] FAD wrong geometry in F-90 project FyD (Sat Nov 01 2014 - 13:50:17 PDT)
- Re: [AMBER] Problem regarding Chamber and psf file Jason Swails (Sat Nov 01 2014 - 15:35:39 PDT)
- [AMBER] Fwd: Re: [q4md-fft] FAD wrong geometry in F-90 project FyD (Sat Nov 01 2014 - 22:39:35 PDT)
- Re: [AMBER] restart file position Fabian Glaser (Sun Nov 02 2014 - 05:57:19 PST)
- Re: [AMBER] NVT and NPT ensemble Sangita Kachhap (Sun Nov 02 2014 - 21:07:05 PST)
- [AMBER] Fully random MPI error after updating CentOS from release 6.5 to 6.6 Massimiliano Porrini (Mon Nov 03 2014 - 02:54:20 PST)
- [AMBER] The question about REMD exchange ratio 王漠野 (Mon Nov 03 2014 - 05:12:50 PST)
- [AMBER] Strange behavior AMBER12 IBRAHIM M ABDELRADY (Mon Nov 03 2014 - 07:52:59 PST)
- [AMBER] error message of addLJType of parmed: Action addLJType failed. UnhandledArgumentWarning: 0.0 0.0 sun (Mon Nov 03 2014 - 08:11:57 PST)
- Re: [AMBER] Imaging Daniel Roe (Mon Nov 03 2014 - 10:45:09 PST)
- [AMBER] single dimension PMF calculation joan.montesdeoca.uns.edu.ar (Mon Nov 03 2014 - 16:32:59 PST)
- [AMBER] aMD error maryam azimzadehirani (Mon Nov 03 2014 - 23:23:10 PST)
- [AMBER] Error logs James Starlight (Tue Nov 04 2014 - 00:24:15 PST)
- [AMBER] bug in pmemd softcore TI with SHAKE Hannes Loeffler (Tue Nov 04 2014 - 02:07:39 PST)
- [AMBER] AMBER Question: Setting box angle in tleap 曲 薇 (Wed Nov 05 2014 - 01:22:48 PST)
- [AMBER] AM1-BCC dipole moment CHAMI F. (Wed Nov 05 2014 - 04:20:04 PST)
- [AMBER] H-REMD Mele N. (Wed Nov 05 2014 - 08:20:33 PST)
- Re: [AMBER] problem using pmemd.cuda with barostat=2 option Sorensen, Jesper (Wed Nov 05 2014 - 10:18:57 PST)
- [AMBER] NBCR AMBER Workshop - UCSD - Mon Dec 15th to Thur Dec 18th 2014 - Registration open. Ross Walker (Wed Nov 05 2014 - 12:40:05 PST)
- [AMBER] cpptraj hist 3D CHAMI F. (Thu Nov 06 2014 - 04:54:58 PST)
- [AMBER] Binding energy using mm_pbsa.pl Wong, Sook (NIH/NCATS) [V] (Thu Nov 06 2014 - 08:28:57 PST)
- [AMBER] determine free available space in simulation box Iqbal, Muhammad Sajid (Thu Nov 06 2014 - 11:04:12 PST)
- [AMBER] Problems on PRMTOP file generation under ff02pol.r1 Wei Ye (Thu Nov 06 2014 - 20:09:02 PST)
- [AMBER] DRUG_PROTEIN INTERACTIOM Ruchika Bhat (Thu Nov 06 2014 - 22:53:11 PST)
- [AMBER] bond distances in amber Mary Varughese (Fri Nov 07 2014 - 01:47:53 PST)
- [AMBER] hbonds Mary Varughese (Fri Nov 07 2014 - 02:27:10 PST)
- [AMBER] Help needed regarding Ligand Protein MD studies Ruchika Bhat (Fri Nov 07 2014 - 05:39:07 PST)
- [AMBER] writing out restart files in netcdf format Sylvester Tumusiime (Fri Nov 07 2014 - 08:24:41 PST)
- [AMBER] HEAT and PROD files for 10 ns run Ruchika Bhat (Sat Nov 08 2014 - 08:45:44 PST)
- [AMBER] simulation of peptide in alkane slab samarprit chakraborty (Sat Nov 08 2014 - 09:43:30 PST)
- Re: [AMBER] Implicit simulation and MMPBSA/GBSA caculations Bajarang Kumbhar (Sat Nov 08 2014 - 22:26:51 PST)
- [AMBER] Which force field is "the best" Gonzalo Jimenez (Sun Nov 09 2014 - 11:10:41 PST)
- [AMBER] MMPBSA.py Sourav Purohit (Sun Nov 09 2014 - 11:20:22 PST)
- [AMBER] Issue with DFTB-MD trajectory Perry, Jamin W. (Sun Nov 09 2014 - 14:02:08 PST)
- [AMBER] Problems of pdb file convertion by pdb4amber and mmtsb LI An-Bang (Sun Nov 09 2014 - 18:31:43 PST)
- [AMBER] a problem on heating the system ZHAO Ruisheng (Mon Nov 10 2014 - 05:25:56 PST)
- [AMBER] Transition state John Smith (Mon Nov 10 2014 - 10:13:36 PST)
- [AMBER] Constant pH MD with CUDA not working BATUHAN KAV (Mon Nov 10 2014 - 12:05:55 PST)
- [AMBER] small molecules Lara rajam (Mon Nov 10 2014 - 12:46:02 PST)
- [AMBER] Representing Sphere and Its parameterization in Amber. ATUL KUMAR (Mon Nov 10 2014 - 22:42:50 PST)
- [AMBER] problem reimaging after strip WAT Pablo D. Dans Puiggròs (Tue Nov 11 2014 - 07:24:34 PST)
- [AMBER] nativecontacts in ambertools14 Asmita Gupta (Tue Nov 11 2014 - 09:03:31 PST)
- [AMBER] cpptraj Sylvester Tumusiime (Tue Nov 11 2014 - 11:30:23 PST)
- [AMBER] options "-ext" and "-pqr" of ambpdb are exlusive LI An-Bang (Tue Nov 11 2014 - 19:48:52 PST)
- [AMBER] [Amber] Amber14 does not find parameters for Mg2+, please help Genin, Nicolas J (Wed Nov 12 2014 - 07:35:49 PST)
- [AMBER] time correlation function giulia palermo (Wed Nov 12 2014 - 10:04:00 PST)
- [AMBER] Running explicit solvent CpHMD on GPUs Garrido Ruiz, Diego (Wed Nov 12 2014 - 11:40:52 PST)
- [AMBER] help Robin Jain (Wed Nov 12 2014 - 21:59:24 PST)
- [AMBER] The question about REMD exchange ratio 王漠野 (Wed Nov 12 2014 - 22:43:55 PST)
- [AMBER] help in MD Robin Jain (Wed Nov 12 2014 - 23:48:20 PST)
- [AMBER] Transition state Mahmood Jasim (Thu Nov 13 2014 - 01:43:51 PST)
- [AMBER] Calcium parameters in calmodulin bharat lakhani (Thu Nov 13 2014 - 08:16:59 PST)
- [AMBER] error in mmpbsa calculation Abdul wadood (Thu Nov 13 2014 - 08:30:40 PST)
- [AMBER] minimization problem Emilio Angelina (Thu Nov 13 2014 - 12:52:28 PST)
- [AMBER] Amber 14 installation problems 汪小涧 (Thu Nov 13 2014 - 19:07:29 PST)
- [AMBER] Entropy using Nmode Wong, Sook (NIH/NCATS) [V] (Fri Nov 14 2014 - 10:57:38 PST)
- [AMBER] Postdoctoral Position at the U.S. Army Research Laboratory in Coarse-Grain Modeling and Simulation Izvyekov, Sergiy (Sergey) CIV USARMY ARL (US) (Fri Nov 14 2014 - 13:11:51 PST)
- [AMBER] pmemd.MPI thermodynamic integration (TI) relative binding free energy set up psu4.uic.edu (Fri Nov 14 2014 - 14:32:49 PST)
- [AMBER] Is there a tool to calculate electron density maps averaged over a trajectory? Jose Borreguero (Fri Nov 14 2014 - 15:16:10 PST)
- Re: [AMBER] GPU enabled Hardware specification M. Reza Ganjalikhany (Sat Nov 15 2014 - 02:41:01 PST)
- [AMBER] heme amber parameter Fatemeh Sadat Alavi (Sat Nov 15 2014 - 07:56:27 PST)
- [AMBER] Prmtop Sylvester Tumusiime (Sat Nov 15 2014 - 08:55:40 PST)
- [AMBER] Failure of antechamber with c -1 m 2 Francesco Pietra (Sun Nov 16 2014 - 09:35:45 PST)
- [AMBER] MMPBSA.py nmode Sourav Purohit (Sun Nov 16 2014 - 18:13:37 PST)
- [AMBER] 4x GTX 980 Parker de Waal (Sun Nov 16 2014 - 18:28:07 PST)
- [AMBER] MMPBSA warning : No skew or curtosis when zero variance in moment Mina Madah (Mon Nov 17 2014 - 00:23:22 PST)
- [AMBER] Regarding pairdist function in cpptraj DEBOSTUTI GHOSHDASTIDAR (Mon Nov 17 2014 - 06:49:06 PST)
- [AMBER] MMPBSA.py normal mode analysis Sourav Purohit (Mon Nov 17 2014 - 12:00:19 PST)
- [AMBER] ERROR DURING "TESTING" OF AMBER INSTALLATION ROOPALI VERMA (Mon Nov 17 2014 - 23:47:31 PST)
- [AMBER] amber error about protein containing heme Fatemeh Sadat Alavi (Tue Nov 18 2014 - 02:31:57 PST)
- [AMBER] amber error about protein containing heme Fatemeh Sadat Alavi (Tue Nov 18 2014 - 02:37:16 PST)
- [AMBER] citation for mdout_analyser.py Krisztina Feher (Tue Nov 18 2014 - 05:14:33 PST)
- [AMBER] tleap not found in parallel amber14 Amihai (Tue Nov 18 2014 - 06:12:45 PST)
- Re: [AMBER] AMBER Digest, Vol 1041, Issue 1 Robin Jain (Tue Nov 18 2014 - 07:34:02 PST)
- [AMBER] nmr restraints and periodic boundary conditions Chris Moth (Tue Nov 18 2014 - 14:20:06 PST)
- [AMBER] InputError when running MMBPSA.py HERBERT MAX VENTHUR PE¥A (Tue Nov 18 2014 - 18:16:54 PST)
- [AMBER] Is it possible to extract atomic charge information from the trajectory? Yip Yew Mun (Tue Nov 18 2014 - 18:53:20 PST)
- [AMBER] Help generating Heme parameters 杨川 (Tue Nov 18 2014 - 23:20:29 PST)
- [AMBER] box size changing during equilibration Robin Jain (Wed Nov 19 2014 - 07:20:29 PST)
- [AMBER] Pairwise vs Sander with imin=5 kurisaki (Wed Nov 19 2014 - 18:01:08 PST)
- [AMBER] ERROR atom with mass 1 has type alreadydesignated as non-hydrogen type Abhishek TYAGI (Wed Nov 19 2014 - 19:01:08 PST)
- [AMBER] Error in CHAMBER output Abhishek TYAGI (Wed Nov 19 2014 - 22:18:25 PST)
- [AMBER] Reminder: NBCR AMBER Workshop - UCSD - Mon Dec 15th to Thur Dec 18th 2014 - Registration open. Ross Walker (Wed Nov 19 2014 - 21:39:51 PST)
- [AMBER] Problems with AmberTools test suite David A Case (Thu Nov 20 2014 - 08:15:31 PST)
- [AMBER] Errors compiling Amber 14 after applying update 7 Bob Healey (Thu Nov 20 2014 - 09:45:08 PST)
- [AMBER] PBSA error Kshatresh Dutta Dubey (Thu Nov 20 2014 - 10:10:08 PST)
- [AMBER] Can you use cholesterol lipid 11 parameters and lipid 14 lipid parameters? Jonathan Gough (Thu Nov 20 2014 - 12:06:19 PST)
- [AMBER] MMPBSA.py bug with amber mask for stability/QH calculations Lawrenz, Morgan (Thu Nov 20 2014 - 15:34:06 PST)
- [AMBER] The error when install amber12+AmberTools13 on Ubuntucd Biao Ma (Thu Nov 20 2014 - 18:31:18 PST)
- [AMBER] cut value in minimisation Robin Jain (Thu Nov 20 2014 - 23:17:49 PST)
- [AMBER] Bug Report Liu, Hui (Thu Nov 20 2014 - 23:38:52 PST)
- [AMBER] cyclic peptide side chains Maria Diaz (Fri Nov 21 2014 - 02:43:50 PST)
- [AMBER] about nab m13654940810 (Fri Nov 21 2014 - 03:12:07 PST)
- [AMBER] Issues with Cholesterol lipid11, lipid14 and lipid14_supp.lib Jonathan Gough (Fri Nov 21 2014 - 10:15:02 PST)
- [AMBER] Questions regarding GB simulations in Amber14 - ff14SBonlysc vs ff14SB - igb1 vs igb8 - hydrphobic force Marek Maly (Fri Nov 21 2014 - 17:58:14 PST)
- Re: [AMBER] AMBER Digest, Vol 1045, Issue 1 Robin Jain (Sat Nov 22 2014 - 00:25:58 PST)
- [AMBER] AMBER error: peek_ewald_inpcrd: SHOULD NOT BE HERE Hadeer ELHabashy (Sat Nov 22 2014 - 07:43:24 PST)
- [AMBER] Installation error: recipe for target 'pupildata.o' failed Parker de Waal (Sat Nov 22 2014 - 14:37:30 PST)
- [AMBER] AMBER Unique atom types Brittany Boykin (Sat Nov 22 2014 - 14:45:39 PST)
- [AMBER] How to seperate a protein-protein complex in PRMTOP and INPCRD files? LI An-Bang (Sun Nov 23 2014 - 16:27:56 PST)
- Re: [AMBER] AMBER Digest, Vol 1044, Issue 1 Abhishek TYAGI (Sun Nov 23 2014 - 22:08:48 PST)
- [AMBER] errors in qm/mm Ayesha Fatima (Sun Nov 23 2014 - 22:10:57 PST)
- [AMBER] Counseling about the GPU series supporting PMEMD geyushu.ustc.edu.cn (Sun Nov 23 2014 - 23:06:03 PST)
- [AMBER] Glycan bond error leap maryam azimzadehirani (Mon Nov 24 2014 - 00:11:31 PST)
- [AMBER] Forcefield for DNA Baifan Wang (Mon Nov 24 2014 - 06:55:15 PST)
- [AMBER] Thermodynamic integration: Delta G of less soft core atoms is different from the one with more soft core atoms sun (Mon Nov 24 2014 - 08:10:22 PST)
- [AMBER] confirm b31b76c2dc0c4f0c33e4cac638252d6c6723f46d Zgarbova Marie (Mon Nov 24 2014 - 12:56:57 PST)
- [AMBER] CHAMBER error Abhishek TYAGI (Mon Nov 24 2014 - 20:37:46 PST)
- [AMBER] doubt in RMD Mary Varughese (Mon Nov 24 2014 - 23:57:32 PST)
- [AMBER] hydophobicity Mary Varughese (Mon Nov 24 2014 - 23:59:24 PST)
- [AMBER] Different PCA results when loading trajectories in a different order Guillaume Roellinger (Tue Nov 25 2014 - 09:49:05 PST)
- [AMBER] How to restrain atoms Akihiro Yamane (Tue Nov 25 2014 - 22:03:13 PST)
- [AMBER] Free energy landscape anu chandra (Wed Nov 26 2014 - 03:07:19 PST)
- [AMBER] AmberTools13 Ibrahim Said (Wed Nov 26 2014 - 09:32:44 PST)
- [AMBER] GTX 780 Ti & GTX 980 Jordi Bujons (Wed Nov 26 2014 - 09:35:06 PST)
- [AMBER] Fw: Elham tazikeh (Thu Nov 27 2014 - 00:57:29 PST)
- [AMBER] Amber 14 and NetCDF installation issue Fernando Ezequiel Chain (Thu Nov 27 2014 - 01:14:37 PST)
- [AMBER] xLEaP Na+ Cl- Weinzierl, Robert O J (Thu Nov 27 2014 - 04:01:03 PST)
- [AMBER] Interaction energy between two dimer unit Soumendranath Bhakat (Thu Nov 27 2014 - 21:26:21 PST)
- [AMBER] installing amber12 in GPU Vijay Achari (Fri Nov 28 2014 - 05:49:35 PST)
- [AMBER] minimization question Carlos Romero (Fri Nov 28 2014 - 07:03:37 PST)
- [AMBER] Correct script for B-factor Soumendranath Bhakat (Fri Nov 28 2014 - 07:38:19 PST)
- [AMBER] QM/MM adaptive biased MD_ABMD Aixiao Li (Fri Nov 28 2014 - 08:36:12 PST)
- [AMBER] generate topology file and parameter file for complex with dummy atoms Jorgen Simonsen (Fri Nov 28 2014 - 15:45:21 PST)
- [AMBER] Calcium vdW parameters Caitlin Scott (Fri Nov 28 2014 - 16:14:40 PST)
- [AMBER] Metal parameterization sailu (Fri Nov 28 2014 - 20:50:46 PST)
- [AMBER] Monitoring pi-cationic interaction asdda asa (Fri Nov 28 2014 - 23:12:14 PST)
- [AMBER] PARALLEL INSTALLATION ERROR Nalini Chauhan (Sun Nov 30 2014 - 03:47:23 PST)
- [AMBER] 100ps long minimization script pradeep pant (Sun Nov 30 2014 - 05:38:01 PST)
- [AMBER] Problem with triangular point in parameter file Jorgen Simonsen (Sun Nov 30 2014 - 09:52:56 PST)
- Last message date: Sun Nov 30 2014 - 15:00:02 PST
- Archived on: Fri Apr 19 2024 - 05:54:47 PDT
