Amber Archive Dec 2020 by thread
- Re: [AMBER] TI electrostatic free energy Franz Waibl (Tue Dec 01 2020 - 04:57:37 PST)
- [AMBER] pmemd.cuda: error while loading shared libraries: libgfortran.so.4: cannot open shared object file: No such file or directory Sruthi Sudhakar (Tue Dec 01 2020 - 05:29:39 PST)
- Re: [AMBER] TI electrostatic free energy] David A Case (Tue Dec 01 2020 - 06:08:32 PST)
- [AMBER] MMBSA.py.MPI installation Jose Manuel Granadino Roldán (Tue Dec 01 2020 - 07:40:03 PST)
- [AMBER] C++ Programmer Position Lachele Foley (Tue Dec 01 2020 - 09:57:01 PST)
- [AMBER] amber 20 compilation problem Jordi Bujons (Tue Dec 01 2020 - 10:14:23 PST)
- [AMBER] question about dihedral angles Gordon Richard Chalmers (Tue Dec 01 2020 - 15:43:50 PST)
- [AMBER] Imaging issue in DNA - cpptraj Satyaseelan C (Tue Dec 01 2020 - 23:17:22 PST)
- Re: [AMBER] NOE analysis with cpptraj Pavlína Pokorná (Wed Dec 02 2020 - 04:27:56 PST)
- [AMBER] Terminal O5'/O3' for nucleosides in ff86? Kenneth Huang (Wed Dec 02 2020 - 14:27:09 PST)
- [AMBER] How to use GAFF2? Alexander Izvorski (Wed Dec 02 2020 - 17:41:08 PST)
- [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA 贺俊宏 (Wed Dec 02 2020 - 19:29:29 PST)
- [AMBER] Mixing Force Constants In DISANG Files Sharif Nada (Wed Dec 02 2020 - 20:01:35 PST)
- [AMBER] app.run_mmpbsa() and mdout files were not created divyabharathi korlepara (Wed Dec 02 2020 - 23:39:11 PST)
- Re: [AMBER] MMPBSA.py bad atom type: M1 error Vaibhav Dixit (Thu Dec 03 2020 - 08:30:11 PST)
- [AMBER] MMPBSA.py.MPI parallel installation using run_cmake divyabharathi korlepara (Thu Dec 03 2020 - 10:43:50 PST)
- [AMBER] Calculation halted while running simulation angad sharma (Thu Dec 03 2020 - 11:36:21 PST)
- [AMBER] Missing Iron (Fe) DFTB3 parameters for QM/MM simulation of Enzyme Hafiz Saqib Ali (Thu Dec 03 2020 - 15:04:54 PST)
- [AMBER] G quadruplex ions minimization Jisha B (Thu Dec 03 2020 - 15:06:25 PST)
- Re: [AMBER] An error during NPT/production (GPU run) David A Case (Fri Dec 04 2020 - 08:13:15 PST)
- Re: [AMBER] amber 20 compilation problem (David A Case) Jordi Bujons (Fri Dec 04 2020 - 09:30:28 PST)
- [AMBER] Question about atomic charges Pinky Mazumder (Fri Dec 04 2020 - 11:15:44 PST)
- Re: [AMBER] ABMD NFE queries Feng Pan (Fri Dec 04 2020 - 17:31:31 PST)
- Re: [AMBER] Regarding to the parameters setup in SMD simulation Feng Pan (Fri Dec 04 2020 - 17:38:11 PST)
- [AMBER] Identifying the equilibrated production region of a MD simulation trajectory Leena Aggarwal (Fri Dec 04 2020 - 23:37:42 PST)
- [AMBER] error after simulation angad sharma (Mon Dec 07 2020 - 08:44:37 PST)
- Re: [AMBER] Tri-coordination environment in zinc Pengfei Li (Mon Dec 07 2020 - 12:29:29 PST)
- [AMBER] lj1264 in vacuum Brian Radak (Tue Dec 08 2020 - 13:29:25 PST)
- Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? David Cerutti (Wed Dec 09 2020 - 00:57:45 PST)
- [AMBER] Regarding Ions renumbering. DHEERAJ CHITARA (Wed Dec 09 2020 - 12:12:18 PST)
- [AMBER] Regarding Gaussian Accelerated MD Sruthi Sudhakar (Wed Dec 09 2020 - 03:16:12 PST)
- [AMBER] Negative values in RDF analyses? Gustaf Olsson (Wed Dec 09 2020 - 05:44:49 PST)
- [AMBER] B-ob-si-c3 dihedral parametization RESP/Scan problem Erdem Yeler (Thu Dec 10 2020 - 02:22:30 PST)
- [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Vaibhav Dixit (Wed Dec 09 2020 - 23:26:05 PST)
- [AMBER] How to proceed if system charge is non-zero and non-integral Amit Sharma (Asstt. Prof., MCARS) (Thu Dec 10 2020 - 04:37:14 PST)
- [AMBER] Bug AmberTools20 parallel installation Arsene Marian Alain (Thu Dec 10 2020 - 04:46:00 PST)
- [AMBER] Charged species with antechamber Sam Walsworth (Researcher) (Thu Dec 10 2020 - 07:01:34 PST)
- [AMBER] tleap building a peptide Seibold, Steve Allan (Thu Dec 10 2020 - 08:48:09 PST)
- [AMBER] how to convert (psf) to (prmtop) and (incprd) Pinky Mazumder (Thu Dec 10 2020 - 22:40:38 PST)
- Re: [AMBER] cellulose crystal structure ( cellulose bundles) Pinky Mazumder (Thu Dec 10 2020 - 22:50:29 PST)
- [AMBER] Box info not found in prmtop file Amit Sharma (Asstt. Prof., MCARS) (Fri Dec 11 2020 - 05:13:38 PST)
- [AMBER] S2 order parameter not being calculated in IRED analysis. Chetna Tyagi (Fri Dec 11 2020 - 05:14:44 PST)
- [AMBER] tleap seems Si atom as S ... I don't know why Erdem Yeler (Fri Dec 11 2020 - 13:58:01 PST)
- [AMBER] MMPBSA.py.MPI not build in Amber20 Setyanto Md (Sat Dec 12 2020 - 05:08:54 PST)
- [AMBER] Hydrogen bond and Dissociation constant Kehinde Idowu (Sat Dec 12 2020 - 06:32:28 PST)
- [AMBER] How to specify SHAKE on all bonds including hydrogen in the input file Amit Sharma (Asstt. Prof., MCARS) (Sat Dec 12 2020 - 10:46:18 PST)
- [AMBER] refene2.solvent_energies refene2.dielc2_energies and refene2.dielc2.solvent_energies Luis Simon (Sat Dec 12 2020 - 15:03:01 PST)
- [AMBER] parameters for benzene, pyerene, anthracene, and coronene Boutheïna KERKENI (Sat Dec 12 2020 - 15:26:24 PST)
- [AMBER] Error in Quasi-Harmonic Entropy Setyanto Md (Sat Dec 12 2020 - 19:09:05 PST)
- [AMBER] Stacking distance in CPPTRAJ Athena N (Sun Dec 13 2020 - 03:18:28 PST)
- [AMBER] Disulphide bonds Gustaf Olsson (Mon Dec 14 2020 - 00:54:19 PST)
- [AMBER] RMSD Protein-DNA complex Plot Manisha (Mon Dec 14 2020 - 01:16:06 PST)
- [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit (Sun Dec 13 2020 - 22:31:52 PST)
- [AMBER] parameters for benzene, pyerene, anthracene, and coronene Boutheïna KERKENI (Mon Dec 14 2020 - 02:20:11 PST)
- [AMBER] box_dims question Carlos (Mon Dec 14 2020 - 13:06:02 PST)
- [AMBER] error finding MMPBSA.py.MPI redirected to amber18 instead of amber20 Vaibhav Dixit (Tue Dec 15 2020 - 09:04:26 PST)
- [AMBER] VDWAALS energy shoots up suddenly during transition from Minimization to Heating Chris Lee (Tue Dec 15 2020 - 15:00:32 PST)
- Re: [AMBER] Amber 4/pre Amber 7 binaries? Bill Ross (Tue Dec 15 2020 - 20:20:18 PST)
- [AMBER] Getting error while compile AMBER20 with cuda support Raman Jangra (Tue Dec 15 2020 - 21:16:10 PST)
- [AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi (Tue Dec 15 2020 - 22:20:02 PST)
- [AMBER] ambpdb or other scipt? Jisha B (Tue Dec 15 2020 - 23:23:23 PST)
- [AMBER] Top Mode Contribution in PCA Analysis. DHEERAJ CHITARA (Wed Dec 16 2020 - 03:53:36 PST)
- [AMBER] positive Amber FF energies? Vaibhav Dixit (Wed Dec 16 2020 - 08:31:55 PST)
- [AMBER] MMPBSA.py.MPI installation divyabharathi korlepara (Wed Dec 16 2020 - 10:10:14 PST)
- [AMBER] Antechamber vs R.E.D. Server Sam Walsworth (Researcher) (Wed Dec 16 2020 - 11:30:54 PST)
- [AMBER] nc files contain lesser number of atoms compared to prmtop Sruthi Sudhakar (Wed Dec 16 2020 - 22:16:53 PST)
- [AMBER] Renumbering Gustaf Olsson (Thu Dec 17 2020 - 02:29:26 PST)
- [AMBER] Using sander.MPI in Docker Erdem Yeler (Thu Dec 17 2020 - 05:07:15 PST)
- Re: [AMBER] AMBER Digest, Vol 3215, Issue 1 David A Case (Thu Dec 17 2020 - 05:21:27 PST)
- [AMBER] cpptraj warnings topology flags being ignored Vaibhav Dixit (Thu Dec 17 2020 - 06:35:36 PST)
- [AMBER] Conversion .rst to .inpcrd Eduardo R. Almeida (Thu Dec 17 2020 - 08:19:59 PST)
- [AMBER] pbsa calcerror Neha Gandhi (Thu Dec 17 2020 - 13:28:59 PST)
- [AMBER] strange jump in the rmsd protein complex Vaibhav Dixit (Thu Dec 17 2020 - 23:36:25 PST)
- [AMBER] Cannot minimize structure with sander George Yacu (Fri Dec 18 2020 - 09:56:28 PST)
- [AMBER] Molecular Dynamics Tutorial for Membrane-Bound Proteins in Amber ANDRES IBACACHE (Fri Dec 18 2020 - 12:22:05 PST)
- [AMBER] Minimization Time Limit Error with Sander Aanshi Gandhi (Fri Dec 18 2020 - 12:39:57 PST)
- [AMBER] AMBER20 on Ubuntu 20.04 and CUDA 11.2? Rudy Richardson (Fri Dec 18 2020 - 15:45:57 PST)
- [AMBER] Cpptraj (post-processing rotation) Женя Елизарова (Mon Dec 21 2020 - 02:08:01 PST)
- [AMBER] question pmemd.cuda MYRIAN TORRES RICO (Mon Dec 21 2020 - 04:45:58 PST)
- [AMBER] Query on some old sander inputs (dele, idiel, dielc) Kenneth Huang (Mon Dec 21 2020 - 08:00:37 PST)
- [AMBER] ff15ipq-m force field for protein mimetics Lillian Chong (Mon Dec 21 2020 - 12:18:59 PST)
- [AMBER] crystallographic plane Pinky Mazumder (Mon Dec 21 2020 - 21:11:50 PST)
- [AMBER] How to graph CPPTRAJ in (ns) instead of timesteps Maghsoud, Yazdan (Tue Dec 22 2020 - 10:51:03 PST)
- [AMBER] Cation-pi interaction characterization Ramanathan Rajesh (Tue Dec 22 2020 - 11:43:58 PST)
- Re: [AMBER] MD run on GPU machine Carlos Simmerling (Tue Dec 22 2020 - 14:38:31 PST)
- [AMBER] Electrostatic distance plot Sruthi Sudhakar (Tue Dec 22 2020 - 19:58:14 PST)
- [AMBER] how to know degrees of system angad sharma (Wed Dec 23 2020 - 07:09:33 PST)
- [AMBER] Parmed error Jisha B (Wed Dec 23 2020 - 09:55:50 PST)
- [AMBER] CPU versus GPU Divergent Minimizations Matthew Guberman-Pfeffer (Thu Dec 24 2020 - 00:22:37 PST)
- [AMBER] Position of the solute (center of mass) in the simulation box Eduardo R. Almeida (Thu Dec 24 2020 - 05:07:04 PST)
- [AMBER] Has anyone tried and succeeded at compiling Amber 18 with CUDA 11? Homeo Morphism (Fri Dec 25 2020 - 13:23:40 PST)
- [AMBER] Reweighting error in Gaussian accelerated MD- PyReweighting-1D.py Athena N (Sat Dec 26 2020 - 14:17:03 PST)
- [AMBER] Problem forming circular DNA Sebastian S (Sun Dec 27 2020 - 07:52:52 PST)
- [AMBER] SHAKE problem Jonathan Church (Sun Dec 27 2020 - 21:26:32 PST)
- [AMBER] Amber20 Installation Error Li,Haoxi (Mon Dec 28 2020 - 17:32:22 PST)
- [AMBER] CMP-GMP Holly Freedman (Tue Dec 29 2020 - 14:31:59 PST)
- [AMBER] cremer MYRIAN TORRES RICO (Wed Dec 30 2020 - 04:48:16 PST)
- [AMBER] doubt frames simulation MYRIAN TORRES RICO (Thu Dec 31 2020 - 05:02:44 PST)
- [AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card liu kai (Thu Dec 31 2020 - 05:34:05 PST)
- Last message date: Thu Dec 31 2020 - 19:00:02 PST
- Archived on: Mon Nov 25 2024 - 05:55:56 PST
