Amber Archive Jul 2021 by thread
- [AMBER] Cluster RMSD Jenny 148 (Wed Jun 30 2021 - 22:35:37 PDT)
- [AMBER] Warning of sp2 improper torsion from Amber tutorial 1.1.4 "Building Protein Systems in Explicit Water" 王维 (Thu Jul 01 2021 - 02:39:24 PDT)
- Re: [AMBER] Constant pH for large number of titratable residues Jason Swails (Thu Jul 01 2021 - 08:41:55 PDT)
- Re: [AMBER] Error charges ligand having Selenium Dr. Anselm Horn (Thu Jul 01 2021 - 12:34:27 PDT)
- [AMBER] Segmentation Fault Swisher, Justin S (Fri Jul 02 2021 - 11:32:58 PDT)
- [AMBER] MMGBSA bad atom type error not fixed by source code edits Matthew Guberman-Pfeffer (Fri Jul 02 2021 - 23:30:30 PDT)
- [AMBER] To build a single covalent bond in a protein-ligand complex using AMBER18. PRIYANKA PUROHIT (Sat Jul 03 2021 - 00:44:59 PDT)
- [AMBER] MD with emap restraints, restraints have no effect Will Gerrard (Sat Jul 03 2021 - 02:51:42 PDT)
- [AMBER] Using ParmEd to convert gromacs truncated octahedron box to amber amin sagar (Sat Jul 03 2021 - 08:13:25 PDT)
- [AMBER] How can I use desmond trajectory in Amber BAS071501 Anupama KP PhD ANS (Sat Jul 03 2021 - 09:08:12 PDT)
- [AMBER] CompEL in AMBER Abdul-Rashid III Sampaco (Sun Jul 04 2021 - 22:10:21 PDT)
- [AMBER] How to assign/apply the negative lateral pressure to lipid bilayer in AMBER? Amir Zeb (Sun Jul 04 2021 - 22:36:04 PDT)
- [AMBER] A question for cpptraj cluster command Yeng-Tseng Wang (Mon Jul 05 2021 - 11:05:57 PDT)
- [AMBER] Question about bilayer lipid dimension estimation (online tutorial: 1.7 An Amber Lipid Force Field Tutorial: Lipid14) 王维 (Tue Jul 06 2021 - 03:01:32 PDT)
- Re: [AMBER] Estimating protein-protein interactions Daniel Roe (Tue Jul 06 2021 - 06:32:42 PDT)
- [AMBER] RNA chiOL3 tleap and ACPYPE conversion Mandar Kulkarni (Wed Jul 07 2021 - 04:47:50 PDT)
- [AMBER] Where are the parameters for the SCREEN RADII section in prmtop Maximilian Ebert (Wed Jul 07 2021 - 07:15:58 PDT)
- [AMBER] To build a single covalent bond between a protein and a ligand. PRIYANKA PUROHIT (Wed Jul 07 2021 - 23:14:46 PDT)
- [AMBER] Ferrocene simulation Gustaf Olsson (Thu Jul 08 2021 - 01:52:33 PDT)
- [AMBER] Scripting ankita mehta (Thu Jul 08 2021 - 05:12:14 PDT)
- [AMBER] Stop PMEMD Terminated Aborally. Tutorial 1.7 An Amber Lipid Force Field Tutorial: Lipid14. 王维 (Thu Jul 08 2021 - 05:59:47 PDT)
- [AMBER] Running in a loop ankita mehta (Thu Jul 08 2021 - 07:37:40 PDT)
- [AMBER] - Free energy calculations of protein molecule with two binding sites Patil Pranita Uttamrao (Thu Jul 08 2021 - 09:53:52 PDT)
- [AMBER] "idecomp" in pairwise decomposition Víctor Vargas (Thu Jul 08 2021 - 10:11:40 PDT)
- [AMBER] Questions about dPCA. 刘保艳 (Thu Jul 08 2021 - 21:29:47 PDT)
- [AMBER] RNA chiOL3 and LJbb with epsilon-zeta correction Mandar Kulkarni (Fri Jul 09 2021 - 03:02:53 PDT)
- [AMBER] Fortran runtime error: Bad value during integer read Sadaf Rani (Fri Jul 09 2021 - 06:48:06 PDT)
- [AMBER] How to study the redox properties of a partially dried protein Matthew Guberman-Pfeffer (Fri Jul 09 2021 - 13:41:45 PDT)
- [AMBER] Modeling 2D material with a bio-molecule/protein Kashyap, Jatin (Fri Jul 09 2021 - 22:56:47 PDT)
- [AMBER] old PREP-specified impropers Sadaf Rani (Sat Jul 10 2021 - 08:57:05 PDT)
- [AMBER] PCA inconsistency on number of frames Mac Kevin Braza (Sat Jul 10 2021 - 15:53:05 PDT)
- [AMBER] Error in MC/MD+TI ABDUL BASIT (Sat Jul 10 2021 - 22:30:29 PDT)
- [AMBER] installation error: /usr/bin/ld: final link failed: Nonrepresentable section on output jinfeng liu (Sun Jul 11 2021 - 02:30:14 PDT)
- [AMBER] vlimit exceeded for some step Sadaf Rani (Mon Jul 12 2021 - 00:06:18 PDT)
- [AMBER] DNA Strand Broken after minimization Sumon Naskar (Tue Jul 13 2021 - 03:22:44 PDT)
- [AMBER] Reweighting aMD conformations Matthew Guberman-Pfeffer (Tue Jul 13 2021 - 05:54:26 PDT)
- [AMBER] Help with imagining curled protein Matthew Guberman-Pfeffer (Tue Jul 13 2021 - 06:31:03 PDT)
- [AMBER] Is Amber18 compatible with AmberTools21 Francis Acquah (Tue Jul 13 2021 - 07:31:41 PDT)
- [AMBER] Split Coordinate files in Amber Rohanizeidanlou, Sahar (Tue Jul 13 2021 - 10:49:03 PDT)
- [AMBER] MMPBSA.py error with "Error occured on rank 1" Mohamed M. Aboelnga (Wed Jul 14 2021 - 07:34:02 PDT)
- [AMBER] Question of Amber_ Sasaki Shiho Ohno (Wed Jul 14 2021 - 16:14:59 PDT)
- [AMBER] What exactly calculates MMPBSA.py? Farkhad Maksudov (Wed Jul 14 2021 - 16:44:46 PDT)
- [AMBER] [cluster] Not all arguments handled: [ sil Sil avgout Avg avgfmt restart ] 余鸿艳 (Thu Jul 15 2021 - 00:03:05 PDT)
- [AMBER] Error:[cluster] Not all arguments handled: [ sil Sil avgout Avg avgfmt restart ] 余鸿艳 (Thu Jul 15 2021 - 00:06:02 PDT)
- [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large Rana Rehan Khalid (Thu Jul 15 2021 - 13:32:49 PDT)
- [AMBER] MD run on RTX-3070 gpu card is much slower than that on RTX-2080ti jinfeng liu (Thu Jul 15 2021 - 21:40:18 PDT)
- [AMBER] pdb4amber Sadaf Rani (Thu Jul 15 2021 - 23:17:34 PDT)
- [AMBER] Amber Tutorial for QM/MM/MD simulations Neha Verma (Fri Jul 16 2021 - 04:46:15 PDT)
- [AMBER] cudaMemcpy GpuBuffer ERROR Gerardo Zerbetto De Palma (Fri Jul 16 2021 - 09:01:56 PDT)
- [AMBER] pc1 vs pc2 principal component analysis Jenny 148 (Fri Jul 16 2021 - 12:42:29 PDT)
- [AMBER] fitpkaeo.py not reading input from cestats Matthew Guberman-Pfeffer (Sat Jul 17 2021 - 15:40:06 PDT)
- [AMBER] Forcefield for alkyl chain in glycolipid molecule Razil Tahir (Sun Jul 18 2021 - 09:56:19 PDT)
- [AMBER] Building Forcefield for Glycolipid Molecule Razil Tahir (Sun Jul 18 2021 - 10:02:45 PDT)
- [AMBER] sampling issue angad sharma (Sun Jul 18 2021 - 11:28:11 PDT)
- [AMBER] Ligand clustering input .pdb file. Samuele Di Cristofano (Mon Jul 19 2021 - 02:13:50 PDT)
- [AMBER] Structure alteration and shortening of loops using xleap Sruthi Sudhakar (Mon Jul 19 2021 - 04:41:41 PDT)
- [AMBER] Missing mtkpp directory after installation of AmberTools21 Anthony Nash (Mon Jul 19 2021 - 06:37:03 PDT)
- [AMBER] The protonation state model of TYR in CpHMD He, Amy (Mon Jul 19 2021 - 11:14:21 PDT)
- [AMBER] velocity trajectory output Daniel Konstantinovsky (Mon Jul 19 2021 - 12:53:50 PDT)
- [AMBER] adding counterions in cpptraj Rohanizeidanlou, Sahar (Mon Jul 19 2021 - 13:48:31 PDT)
- [AMBER] 3D-RISM in amber20 Priya Dey (Mon Jul 19 2021 - 23:35:08 PDT)
- [AMBER] tleap does not recognize inosine Thamires Rocco Machado (Tue Jul 20 2021 - 07:12:54 PDT)
- [AMBER] MCPB.py 'OW' type error in AmberTools21 David William Kastner (Tue Jul 20 2021 - 07:51:12 PDT)
- [AMBER] Gas phase Simulations Kolattukudy P. Santo (Tue Jul 20 2021 - 11:17:32 PDT)
- [AMBER] Displacement of coordinated Zn during the simulation Amit Sharma (Asstt. Prof., MCARS) (Wed Jul 21 2021 - 08:27:08 PDT)
- [AMBER] Simulating dehydrated bilayers with a vacuum above and below Blake Armstrong (Fri Jul 23 2021 - 00:50:52 PDT)
- [AMBER] Regarding SHAKE Parameter Sumon Naskar (Fri Jul 23 2021 - 03:38:01 PDT)
- [AMBER] gpu error Debarati DasGupta (Fri Jul 23 2021 - 06:25:28 PDT)
- [AMBER] Include specific solvent in constant pH MD simulation by CPHFIRST_SOL He, Amy (Sat Jul 24 2021 - 23:12:27 PDT)
- [AMBER] Protein-protein interaction energy calculation SATYAJIT KHATUA (Sun Jul 25 2021 - 06:33:41 PDT)
- [AMBER] Solvate and manipulate order of atoms in Leap He, Amy (Sun Jul 25 2021 - 15:26:06 PDT)
- [AMBER] Cphstats unable to read cpin Matthew Guberman-Pfeffer (Sun Jul 25 2021 - 20:50:46 PDT)
- [AMBER] SEBOMD topology issue Daniel Konstantinovsky (Mon Jul 26 2021 - 12:03:29 PDT)
- [AMBER] running Free Energy Perturbation with amber20 Laura SCALVINI (Mon Jul 26 2021 - 23:58:30 PDT)
- [AMBER] Convergence issue in 1drism angad sharma (Tue Jul 27 2021 - 11:51:32 PDT)
- [AMBER] questions about unbond parameters 李政新 (Tue Jul 27 2021 - 21:01:00 PDT)
- [AMBER] Installing AmberTools with C++11 support Muhammad Ayaz Anwar (Wed Jul 28 2021 - 02:20:22 PDT)
- [AMBER] MMGBSA CalcError: mmpbsa_py_energy failed with prmtop Maschietto, Federica (Wed Jul 28 2021 - 10:46:46 PDT)
- [AMBER] Physical chemistry question regarding entropy calculations in ligand-receptor system Liao (Wed Jul 28 2021 - 12:33:34 PDT)
- [AMBER] Error message Vento, Gabby (Wed Jul 28 2021 - 14:30:59 PDT)
- [AMBER] Simulation of protein immobilization Markowska (Thu Jul 29 2021 - 05:13:36 PDT)
- [AMBER] unexpected missing parameters for protein atoms? Vaibhav Dixit (Fri Jul 30 2021 - 04:09:08 PDT)
- [AMBER] N_OF_BONDS colvar and PBC Hugo Macdermott-Opeskin (Fri Jul 30 2021 - 17:10:57 PDT)
- Last message date: Sat Jul 31 2021 - 06:00:02 PDT
- Archived on: Fri Dec 20 2024 - 05:56:08 PST
