Amber Archive Nov 2021 by thread
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces Umesh Roy (Sun Oct 31 2021 - 23:40:59 PDT)
- Re: [AMBER] Problem measuring angle in CPPTRAJ Daniel Roe (Mon Nov 01 2021 - 07:05:01 PDT)
- Re: [AMBER] Fwd: Constant pH MD simulation Jason Swails (Mon Nov 01 2021 - 07:09:20 PDT)
- [AMBER] Is there a polarizable counterpart to FF99sb? Matthew Guberman-Pfeffer (Mon Nov 01 2021 - 10:26:00 PDT)
- [AMBER] Installation question Michael Goldstein (Mon Nov 01 2021 - 11:28:18 PDT)
- [AMBER] Restraint-like bonds using ParmEd setBond? Brian Radak (Mon Nov 01 2021 - 11:32:29 PDT)
- [AMBER] Preparing/generating input files for Amber MD Jhuma Das (Mon Nov 01 2021 - 12:32:09 PDT)
- Re: [AMBER] How to Compare RDFs for different systems Thomas Cheatham (Mon Nov 01 2021 - 21:33:01 PDT)
- [AMBER] Question of Amber_ Sasaki Shiho Ohno (Mon Nov 01 2021 - 21:57:12 PDT)
- [AMBER] NVT or NPT in aMD simulations? Michael Shokhen (Tue Nov 02 2021 - 02:15:51 PDT)
- [AMBER] Error upon start of nfe-abmd Rafał Madaj (Tue Nov 02 2021 - 04:03:53 PDT)
- [AMBER] CartHess2FC Jon Uranga (Tue Nov 02 2021 - 04:32:53 PDT)
- [AMBER] How to gradually release the Cartesian restraint? Heng Cao (Tue Nov 02 2021 - 09:59:09 PDT)
- [AMBER] Amber installation error for Intel Xeon machine (ubuntu 20.04) Chen, Guoquan (Tue Nov 02 2021 - 14:51:25 PDT)
- [AMBER] about pmemd.cuda 田佳琪 (Tue Nov 02 2021 - 20:55:13 PDT)
- [AMBER] Inquiry on CPPTRAJ Razil Tahir (Tue Nov 02 2021 - 21:13:02 PDT)
- [AMBER] ParmEd error Sangeetha B (Wed Nov 03 2021 - 04:39:22 PDT)
- [AMBER] Multiple Replicate Trajectories Li,Haoxi (Wed Nov 03 2021 - 06:40:50 PDT)
- [AMBER] Amber MD NAN (1-4 NB = ************** 1-4 EEL = ************** ) mish (Wed Nov 03 2021 - 09:52:19 PDT)
- [AMBER] CUDA INSTALLATION FAILED (Error: Symbol ‘atompositions_fce’ at (1) has no IMPLICIT type) Akash Deep Biswas (Thu Nov 04 2021 - 04:38:09 PDT)
- [AMBER] Defining a new atom type (metal) Sam Walsworth (Researcher) (Thu Nov 04 2021 - 08:12:23 PDT)
- [AMBER] end state in TI calculations with pmemd.cuda Qinghua Liao (Thu Nov 04 2021 - 08:21:09 PDT)
- [AMBER] water box corrupted by minimization Michael Shokhen (Thu Nov 04 2021 - 10:07:41 PDT)
- [AMBER] Amber calculate RMSF 吴晓东 (Thu Nov 04 2021 - 17:29:51 PDT)
- [AMBER] antechamber use for two unit ligand Rana Rehan Khalid (Fri Nov 05 2021 - 13:30:08 PDT)
- [AMBER] Ligand breaks during system preparation Ch Bilal (Sat Nov 06 2021 - 00:02:48 PDT)
- [AMBER] Could tleap read in parameter and restart file instead of PDB or mol2? Liao (Sat Nov 06 2021 - 13:15:55 PDT)
- [AMBER] question of Amber calculate RMSF 吴晓东 (Sun Nov 07 2021 - 00:45:55 PDT)
- [AMBER] How to generate the .mol2 and .frcmod files for a carbohydrate with GLYCAM06 atom types in Antechamber Bhat Zahoor (Sun Nov 07 2021 - 01:48:23 PST)
- [AMBER] 【MCPB】 Why is the wrong file generated in tleap.in Huimin Tian (Mon Nov 08 2021 - 00:36:23 PST)
- [AMBER] cpptraj error with github version ubuntu 20.04 Vaibhav Dixit (Mon Nov 08 2021 - 01:31:17 PST)
- [AMBER] 【MCPB】 Why is the wrong file generated in tleap.in Huimin Tian (Mon Nov 08 2021 - 02:04:08 PST)
- [AMBER] Cellulose-COOH modification Arash Elahi (Mon Nov 08 2021 - 19:57:11 PST)
- [AMBER] How to change a Histidine protonation state Sadaf Rani (Tue Nov 09 2021 - 02:05:16 PST)
- [AMBER] Hydrogen Mass Repartitioning without ParmEd ABEL Stephane (Tue Nov 09 2021 - 05:49:40 PST)
- [AMBER] How to generate only CA (alpha) atoms trajectory in cpptraj Amber Md Fulbabu Sk (Tue Nov 09 2021 - 08:04:50 PST)
- [AMBER] Using RESP charges in antechamber Sam Walsworth (Researcher) (Tue Nov 09 2021 - 08:43:17 PST)
- [AMBER] Unable to correctly identify element EPW Sai Kumar Ramadugu (Tue Nov 09 2021 - 11:14:22 PST)
- [AMBER] Cellulose-COOH modification Arash Elahi (Tue Nov 09 2021 - 11:41:21 PST)
- [AMBER] How to generate mol2 file with topology and crd file? Eugene huh (Wed Nov 10 2021 - 01:25:17 PST)
- [AMBER] Error running metalpdb2mol2 Sam Walsworth (Researcher) (Wed Nov 10 2021 - 03:45:36 PST)
- [AMBER] Warnings for sp2 for two improper dihedrals ABEL Stephane (Wed Nov 10 2021 - 06:07:02 PST)
- [AMBER] scientific issue SOMA ROY (Wed Nov 10 2021 - 07:11:21 PST)
- [AMBER] CPPTRAJ Rana Rehan Khalid (Wed Nov 10 2021 - 10:38:18 PST)
- [AMBER] ion concentration 150mM NaCl in King Wu (Wed Nov 10 2021 - 22:11:50 PST)
- [AMBER] Isopeptide bond parameterization Venkatareddy Dadireddy (Thu Nov 11 2021 - 05:51:34 PST)
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 Daniel Roe (Thu Nov 11 2021 - 06:18:16 PST)
- [AMBER] INFO Steered Molecular Dynamics Francesca Di Matteo - francesca.dimatteo5.studio.unibo.it (Thu Nov 11 2021 - 07:12:04 PST)
- [AMBER] amber20 - cmake cannot find cuda Fabian Glaser (Thu Nov 11 2021 - 08:21:51 PST)
- [AMBER] tleap problem Debarati DasGupta (Thu Nov 11 2021 - 13:11:51 PST)
- [AMBER] Regarding setting up MMGBSA calculation Debarati DasGupta (Fri Nov 12 2021 - 04:18:24 PST)
- [AMBER] Running Simulations in a Vacuum Juliette Newell (Fri Nov 12 2021 - 04:33:51 PST)
- [AMBER] Post-doc opportunity Pratul Agarwal (Fri Nov 12 2021 - 10:48:27 PST)
- [AMBER] S-adenosyl-L-methionine (SAM) ff parameters Venkatareddy Dadireddy (Fri Nov 12 2021 - 20:53:39 PST)
- Re: [AMBER] Building Forcefield for Glycolipid Molecule Razil Tahir (Fri Nov 12 2021 - 22:37:51 PST)
- [AMBER] What ion parameters can be used with non-water solvents? Matthew Guberman-Pfeffer (Fri Nov 12 2021 - 23:42:05 PST)
- [AMBER] MMGBSA error mitigation Debarati DasGupta (Sat Nov 13 2021 - 05:16:03 PST)
- [AMBER] when SLEAP got dropped? Alan (Sun Nov 14 2021 - 10:51:28 PST)
- [AMBER] Using mmpbsa_py_nabnmode directly Liao (Sun Nov 14 2021 - 12:29:43 PST)
- [AMBER] Functional error Archana (Sun Nov 14 2021 - 22:49:24 PST)
- [AMBER] help, we are frequently face this error zeinab masoomi (Mon Nov 15 2021 - 01:22:17 PST)
- [AMBER] GIST: Entropy calculations Umesh Roy (Mon Nov 15 2021 - 02:19:32 PST)
- [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ? ABEL Stephane (Mon Nov 15 2021 - 05:11:52 PST)
- [AMBER] Compilation error Ruibin Liu (Tue Nov 16 2021 - 07:03:23 PST)
- [AMBER] Bug Encountered When sourcing GAFF in leap.in Vollmers, Luis (Tue Nov 16 2021 - 07:28:27 PST)
- [AMBER] parametrization with fixed charges on some atoms Reza Esmaeeli (Tue Nov 16 2021 - 16:03:24 PST)
- [AMBER] Compilation Instructions for Mac M1? Brandon Orzolek (Tue Nov 16 2021 - 17:05:03 PST)
- [AMBER] Entropy by quasi harmonic approximations on multiple CPU ABDUL BASIT (Tue Nov 16 2021 - 20:49:59 PST)
- [AMBER] Electrostatic energy in a simple non-periodic system Ali Morshedi (Wed Nov 17 2021 - 00:53:31 PST)
- [AMBER] Dynamic cross correlation matrices in AMBER20 Debarati DasGupta (Wed Nov 17 2021 - 08:50:00 PST)
- [AMBER] Parameterize small molecules with CGenFF in Amber He, Amy (Wed Nov 17 2021 - 11:56:58 PST)
- [AMBER] ParmEd: tiMerge error with ff19SB CMAP term Ali Morshedi (Thu Nov 18 2021 - 01:06:54 PST)
- Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ? --update ABEL Stephane (Thu Nov 18 2021 - 04:23:18 PST)
- [AMBER] How to add an amidated residue at the C-terminal in AMBER tleap ? Yen Nguyen (Thu Nov 18 2021 - 11:47:43 PST)
- [AMBER] How to create a MOH box (only methanol molecules) Alan (Thu Nov 18 2021 - 14:17:43 PST)
- [AMBER] SelectionError: Invalid selection. Illegal residue range Nousheen (Fri Nov 19 2021 - 02:06:00 PST)
- [AMBER] xLEaP Keyboard? Brandon Orzolek (Fri Nov 19 2021 - 12:02:28 PST)
- [AMBER] Summit compile and "Attempted to read inpcrd as a NetCDF restart file, but failed" Derek M Shore (Fri Nov 19 2021 - 15:56:21 PST)
- [AMBER] Error: In _MMPBSA_complex.mdcrd.0, expect only 3 or 6 box coords, got 5 Akinyemi Omoniyi (Sat Nov 20 2021 - 16:47:45 PST)
- [AMBER] problems with FEP calculations Małgorzata Kogut (Mon Nov 22 2021 - 06:45:25 PST)
- [AMBER] amber20 - test suite picks up the wrong libgfortran Mark Dixon (Mon Nov 22 2021 - 09:12:07 PST)
- [AMBER] "unknown flag: filename.top" error with PMEMD and topology file from CHARMM-GUI Chris Lee (Mon Nov 22 2021 - 17:25:27 PST)
- [AMBER] Interesting findings regarding water density, ntf values, and total potential energy Liao (Tue Nov 23 2021 - 00:23:35 PST)
- [AMBER] Available postdoctoral position Reza Khayat (Tue Nov 23 2021 - 11:12:43 PST)
- [AMBER] Protein in mixed of solvents Damiano Spadoni (Tue Nov 23 2021 - 12:26:45 PST)
- [AMBER] installation error amber 18 in ubuntu 20.04 Ayesha Fatima (Wed Nov 24 2021 - 01:06:09 PST)
- [AMBER] duplicate simulations problem Sadaf Rani (Wed Nov 24 2021 - 02:07:37 PST)
- [AMBER] Lipid17 PGR vs PGS Baker, Joseph (Wed Nov 24 2021 - 09:01:19 PST)
- [AMBER] Equilibrate and Production Run Membrane-protein complex King Wu (Wed Nov 24 2021 - 17:15:40 PST)
- [AMBER] closest ions radiation distribution Vaibhav Dixit (Thu Nov 25 2021 - 01:28:15 PST)
- [AMBER] [MCPB] Why is the wrong file generated in tleap.in Huimin Tian (Thu Nov 25 2021 - 22:54:48 PST)
- [AMBER] Mutation of R to Histidine mohamed marzouk (Fri Nov 26 2021 - 08:13:07 PST)
- [AMBER] How to interpret clustering Sadaf Rani (Fri Nov 26 2021 - 08:16:21 PST)
- [AMBER] RMSD of different protein PDBs Seibold, Steve Allan (Sat Nov 27 2021 - 15:01:50 PST)
- [AMBER] Problems with RMSD of different proteins. Seibold, Steve Allan (Sun Nov 28 2021 - 07:47:10 PST)
- [AMBER] 【tleap】 How to add water(TIP3P) to the right place in the protein？ Huimin Tian (Sun Nov 28 2021 - 18:29:57 PST)
- [AMBER] Partial frame/traj dump during MD run. Pedro Guillem (Mon Nov 29 2021 - 02:52:14 PST)
- [AMBER] different performance with and without distance restraints in TI calculation Qinghua Liao (Mon Nov 29 2021 - 05:07:36 PST)
- [AMBER] interpolated corrections Pedro Miguel Reis Figueiredo (Mon Nov 29 2021 - 05:59:58 PST)
- [AMBER] Regarding two stage resp fittings (Using Gaussian 09 output) Rajarshi Roy (Mon Nov 29 2021 - 06:59:51 PST)
- [AMBER] open mpi compiler error Ayesha Fatima (Mon Nov 29 2021 - 23:50:38 PST)
- [AMBER] Using predefined Ag+ parameters Sam Walsworth (Researcher) (Tue Nov 30 2021 - 05:48:02 PST)
- Last message date: Tue Nov 30 2021 - 13:00:02 PST
- Archived on: Wed Dec 25 2024 - 05:56:09 PST
