Amber Archive Aug 2024 by thread
- Re: [AMBER] production run mdin file Dulal Mondal via AMBER (Thu Aug 01 2024 - 05:10:51 PDT)
- Re: [AMBER] ff99 and ff14SB - Slight Atom Type Differences Carlos Simmerling via AMBER (Thu Aug 01 2024 - 08:42:16 PDT)
- Re: [AMBER] Atom type of DU does not exist in PARMCHK.DAT Abdelrahman, Noureen via AMBER (Thu Aug 01 2024 - 12:58:01 PDT)
- Re: [AMBER] MD simulations for 100 ns and PCA Thomas Cheatham via AMBER (Thu Aug 01 2024 - 23:20:02 PDT)
- Re: [AMBER] Effective Born Radius Jaime Rubio Martinez via AMBER (Sat Aug 03 2024 - 04:30:38 PDT)
- Re: [AMBER] cphstats processing of pH-REMD 'chunks' He, Amy via AMBER (Sun Aug 04 2024 - 16:05:31 PDT)
- [AMBER] No QM parameter for a Sulfur atom Sunanda Samanta via AMBER (Sun Aug 04 2024 - 23:03:28 PDT)
- Re: [AMBER] MCPB.py keyerror Li, Zhen via AMBER (Mon Aug 05 2024 - 08:51:41 PDT)
- [AMBER] CHARMM-GUI-provided scripts HAFIDAH ZAKI AL QUDAH via AMBER (Mon Aug 05 2024 - 12:09:57 PDT)
- [AMBER] Issues with the Glycoprotein builder on the glycamm website Natesan Mani via AMBER (Mon Aug 05 2024 - 14:37:02 PDT)
- Re: [AMBER] SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f> in QUICK Goetz, Andreas via AMBER (Mon Aug 05 2024 - 23:48:41 PDT)
- [AMBER] Amber/AmberTools24 installation Apple M2 Xavier Brazzolotto via AMBER (Tue Aug 06 2024 - 01:24:43 PDT)
- Re: [AMBER] Cmake unable to find Mpich Pertschy, Florian via AMBER (Tue Aug 06 2024 - 08:46:47 PDT)
- [AMBER] MPI installation failing. Pertschy, Florian via AMBER (Tue Aug 06 2024 - 09:18:42 PDT)
- [AMBER] Torsion Term Error Cinar, Sena via AMBER (Tue Aug 06 2024 - 11:55:31 PDT)
- [AMBER] Evaluate change in affinity due to mutation Abhilash J via AMBER (Tue Aug 06 2024 - 12:11:50 PDT)
- [AMBER] different pH conditions for membrane protein simulations Prithviraj Nandigrami via AMBER (Tue Aug 06 2024 - 12:34:58 PDT)
- [AMBER] Tleap error Prabir Khatua via AMBER (Wed Aug 07 2024 - 00:23:03 PDT)
- [AMBER] parameterize a non-standard residue Peng Zhang via AMBER (Wed Aug 07 2024 - 09:12:40 PDT)
- [AMBER] Query about continuous constant pH in amber24 (chapter 28) Dulal Mondal via AMBER (Wed Aug 07 2024 - 20:44:43 PDT)
- [AMBER] Amber24 Cuda installation Pertschy, Florian via AMBER (Thu Aug 08 2024 - 08:07:41 PDT)
- [AMBER] Requesting help with Amber TI calculation Weerawarna Kurukulasooriy, Sandaruwani Tharaka \[CHEM\] via AMBER (Thu Aug 08 2024 - 08:48:07 PDT)
- [AMBER] How to build own system Sepideh Jafari via AMBER (Thu Aug 08 2024 - 09:51:14 PDT)
- [AMBER] Fwd: Regarding Advanced Thermodynamic Integration: Kankana Bhattacharjee via AMBER (Thu Aug 08 2024 - 11:53:48 PDT)
- [AMBER] Surface area of one protein to another King Wang via AMBER (Thu Aug 08 2024 - 13:17:57 PDT)
- Re: [AMBER] Regarding Advanced Thermodynamic Integration: He, Amy via AMBER (Thu Aug 08 2024 - 15:36:04 PDT)
- [AMBER] Error in ligand paramterisation in tleap Simran Modi via AMBER (Fri Aug 09 2024 - 03:23:13 PDT)
- [AMBER] parm10 and PARMCHK.DAT Atom Types Pye, Aaron Wesley via AMBER (Sat Aug 10 2024 - 05:40:04 PDT)
- [AMBER] Amber 24 encounters freezed jobs Morad Mustafa via AMBER (Sun Aug 11 2024 - 08:19:24 PDT)
- [AMBER] finddgref.py error with manually added titratable ligand Nitin Kulhar via AMBER (Sun Aug 11 2024 - 21:30:33 PDT)
- Re: [AMBER] QM/MM produces no error but doesn't run successfully Timothy Giese via AMBER (Mon Aug 12 2024 - 08:57:47 PDT)
- [AMBER] Assistance Needed with PCA at Different Temperatures in AMBER ABDELATIF MESSAOUDI via AMBER (Mon Aug 12 2024 - 11:37:22 PDT)
- [AMBER] Executing absolute binding free energy calculations in Amber Amara Jabeen via AMBER (Tue Aug 13 2024 - 00:59:56 PDT)
- [AMBER] illegal memory access Alois Zdrha via AMBER (Tue Aug 13 2024 - 05:01:55 PDT)
- [AMBER] QM/MM Energy Decomposition Ge Song via AMBER (Tue Aug 13 2024 - 12:28:16 PDT)
- Re: [AMBER] [Sender Not Verified] Re: Requesting help with Amber TI calculation Steinbrecher, Thomas via AMBER (Tue Aug 13 2024 - 23:16:53 PDT)
- [AMBER] Compiling CUDA - gpu compatability Alexander Hung Lee via AMBER (Thu Aug 15 2024 - 11:49:42 PDT)
- [AMBER] FETookit analysis issue: Kankana Bhattacharjee via AMBER (Fri Aug 16 2024 - 00:10:21 PDT)
- [AMBER] query about scaling of nonbonded interactions. Prof. Mark Wilson via AMBER (Fri Aug 16 2024 - 02:10:10 PDT)
- [AMBER] Trouble Calculating Nucleic Pseudo-Torsions Eta and Theta (η-θ) w/ CPPTRAJ Warren, Kyle Benjamin via AMBER (Fri Aug 16 2024 - 07:52:43 PDT)
- [AMBER] Amber22 cudaGetDeviceCount failed unknown error Gustavo Seabra via AMBER (Fri Aug 16 2024 - 08:39:03 PDT)
- [AMBER] Fwd: modifying colvars Gard Nelson via AMBER (Fri Aug 16 2024 - 15:30:18 PDT)
- [AMBER] AmberMDPrep.sh finishes after final.1.in step Maciej Spiegel via AMBER (Sat Aug 17 2024 - 13:57:06 PDT)
- [AMBER] Multiple Replicas per GPU? Guberman-Pfeffer, Matthew via AMBER (Sun Aug 18 2024 - 00:18:53 PDT)
- [AMBER] remlog in cpptraj for pH-REMD Guberman-Pfeffer, Matthew via AMBER (Sun Aug 18 2024 - 10:55:56 PDT)
- [AMBER] Multiple Replicas per GPU? Guberman-Pfeffer, Matthew via AMBER (Sun Aug 18 2024 - 12:02:04 PDT)
- [AMBER] Unclear cphstats warning Guberman-Pfeffer, Matthew via AMBER (Sun Aug 18 2024 - 12:02:31 PDT)
- [AMBER] Missing angle parameter between unconnected atoms Peng Zhang via AMBER (Sun Aug 18 2024 - 14:25:32 PDT)
- [AMBER] Custom AA residue missing parameters Javier O Sanlley-hernandez via AMBER (Mon Aug 19 2024 - 12:39:45 PDT)
- [AMBER] amber19 installation error Dulal Mondal via AMBER (Mon Aug 19 2024 - 13:28:50 PDT)
- [AMBER] 回复: Custom AA residue missing parameters Huang ZiJian via AMBER (Mon Aug 19 2024 - 21:38:55 PDT)
- [AMBER] Free energy calculation of complex with covalent bond SUBHASMITA MAHAPATRA MAHAPATRA via AMBER (Tue Aug 20 2024 - 03:11:02 PDT)
- [AMBER] Cutoff value significantly impacts the electrostatic energy in PME Ge Song via AMBER (Tue Aug 20 2024 - 06:44:12 PDT)
- [AMBER] Per residue energy decomposition RAMPRAKASH YADAV via AMBER (Tue Aug 20 2024 - 22:30:31 PDT)
- [AMBER] Regarding an issue with Thermodynamic Integration calculation Weerawarna Kurukulasooriy, Sandaruwani Tharaka \[CHEM\] via AMBER (Wed Aug 21 2024 - 10:53:03 PDT)
- [AMBER] Convergence checking in Advanced TI calculation: Kankana Bhattacharjee via AMBER (Wed Aug 21 2024 - 20:57:51 PDT)
- [AMBER] packmol-memgen: issue with the parametrization of gpcr-ligand system Enrico Martinez via AMBER (Fri Aug 23 2024 - 01:56:34 PDT)
- [AMBER] Assigning GPUs with pHREMD Guberman-Pfeffer, Matthew via AMBER (Fri Aug 23 2024 - 05:14:43 PDT)
- [AMBER] Extracting every 10th frame from *.nc file Maciej Spiegel via AMBER (Fri Aug 23 2024 - 08:15:27 PDT)
- [AMBER] issue using pemed.cuda of AMBER 24 Abhilash J via AMBER (Fri Aug 23 2024 - 10:38:05 PDT)
- [AMBER] Regarding placement of periodic box Natesan Mani via AMBER (Sat Aug 24 2024 - 10:59:28 PDT)
- [AMBER] combining the results of nab nmode and mmpbsa Siavoush Dastmalchi via AMBER (Sun Aug 25 2024 - 03:38:03 PDT)
- [AMBER] Modeling and simulating a cyclic depsipeptide Baker, Joseph via AMBER (Sun Aug 25 2024 - 08:02:04 PDT)
- [AMBER] run errorn in sander.MPI for constant pH replica exchange in amber18 Dulal Mondal via AMBER (Sun Aug 25 2024 - 23:03:21 PDT)
- [AMBER] MMGBSA Calculation Python --version ABDELATIF MESSAOUDI via AMBER (Mon Aug 26 2024 - 02:03:49 PDT)
- [AMBER] Error to run constant pH replica exchange in explicit solvent in amber18 Dulal Mondal via AMBER (Mon Aug 26 2024 - 10:16:34 PDT)
- [AMBER] Continuous constant pH MD with pH replica exchange Nancy Zhu via AMBER (Mon Aug 26 2024 - 15:13:27 PDT)
- [AMBER] Lone pair treatment AMBER24 Sorin Draga via AMBER (Tue Aug 27 2024 - 02:21:03 PDT)
- [AMBER] Amber to Lammps; velocities conversion Meyer, Olivia \(meyerok\) via AMBER (Tue Aug 27 2024 - 07:59:31 PDT)
- [AMBER] PCA on Unmodified and Modified Nucleobases within RNA: Different Ribose Atom Ordering Warren, Kyle Benjamin via AMBER (Tue Aug 27 2024 - 10:12:03 PDT)
- [AMBER] Protein RNA complex simulation best standards in the field. Debarati DasGupta via AMBER (Tue Aug 27 2024 - 16:16:40 PDT)
- [AMBER] Reply: Re: combining the results of nab nmode and mmpbsa Siavoush Dastmalchi via AMBER (Tue Aug 27 2024 - 22:58:21 PDT)
- [AMBER] Amber22_Error: an illegal memory access was encountered launching kernel kNLSkinTest ABDELATIF MESSAOUDI via AMBER (Wed Aug 28 2024 - 00:52:09 PDT)
- [AMBER] Fwd: TI calculation using pmemd Tamalika Ash via AMBER (Wed Aug 28 2024 - 08:55:12 PDT)
- [AMBER] Computing free energy of binding from advanced TI calculation: Kankana Bhattacharjee via AMBER (Wed Aug 28 2024 - 22:27:45 PDT)
- [AMBER] Modification of MMPBSA electrostatic energy Anupaul Baruah via AMBER (Thu Aug 29 2024 - 03:10:46 PDT)
- [AMBER] Regarding REUS simulations miyagi bunkutu via AMBER (Thu Aug 29 2024 - 12:06:37 PDT)
- [AMBER] About making Amber code a more standard Vlad via AMBER (Thu Aug 29 2024 - 16:37:41 PDT)
- [AMBER] 回复: Custom AA residue missing parameters Huang ZiJian via AMBER (Fri Aug 30 2024 - 00:59:08 PDT)
- [AMBER] Error message : "unsigned long long of length = 42Failed an illegal memory access was encountered" Anna Herz via AMBER (Fri Aug 30 2024 - 07:43:10 PDT)
- Last message date: Fri Aug 30 2024 - 08:30:02 PDT
- Archived on: Mon Oct 14 2024 - 05:56:16 PDT
