Amber Archive Aug 2021: by date

Saturday, 31 July 2021
- [AMBER] Chloride ion atom type issue in tleap Aliakbartehrani Zahra
Sunday, 1 August 2021
- Re: [AMBER] Chloride ion atom type issue in tleap David A Case
- Re: [AMBER] N_OF_BONDS colvar and PBC Feng Pan
Monday, 2 August 2021
- [AMBER] Questions about the TI methods in binding free energy calculations. neildancer.sina.com
- Re: [AMBER] Questions about the TI methods in binding free energy calculations. David A Case
- Re: [AMBER] Questions about the TI methods in binding free energy calculations. neildancer
- [AMBER] Question about using C-F with iRED Darian Yang
Tuesday, 3 August 2021
- Re: [AMBER] Question about using C-F with iRED David A Case
- Re: [AMBER] Solvate and manipulate order of atoms in Leap David A Case
- [AMBER] ERROR: I could not find enough velocities ankita mehta
- [AMBER] Boron containing molecules in GAFF Brian Radak
- [AMBER] Question on Paramfit QM File Swisher, Justin S
- [AMBER] Steered MD simulation Prithvi Raj Pandey
- [AMBER] SolvateOct box volume and cubic box information Umesh Roy
- Re: [AMBER] ERROR: I could not find enough velocities David A Case
- Re: [AMBER] SolvateOct box volume and cubic box information David A Case
- Re: [AMBER] SolvateOct box volume and cubic box information James Kress
- [AMBER] Amber parmeters for ACE-CYX bond Ali Kusay
- Re: [AMBER] SolvateOct box volume and cubic box information Umesh Roy
Wednesday, 4 August 2021
- Re: [AMBER] SolvateOct box volume and cubic box information Carlos Simmerling
- Re: [AMBER] SolvateOct box volume and cubic box information David A Case
- Re: [AMBER] Boron containing molecules in GAFF David A Case
- Re: [AMBER] Boron containing molecules in GAFF Brian Radak
- [AMBER] Freezing atoms in MCPB gaussian small_opt calculations David William Kastner
- Re: [AMBER] SolvateOct box volume and cubic box information Daniel Roe
- Re: [AMBER] Question on Paramfit QM File Robin Betz
- [AMBER] Why is self-correlation with atomiccorr in cpptraj zero? Matthew Guberman-Pfeffer
- Re: [AMBER] SolvateOct box volume and cubic box information James Kress
- Re: [AMBER] SolvateOct box volume and cubic box information Umesh Roy
Thursday, 5 August 2021
- [AMBER] How to visualize the protein-implicit solvent boundary Matthew Guberman-Pfeffer
- [AMBER] Lite Hash Rate and pmemd.cuda Sergei Izmailov
- Re: [AMBER] Amber parmeters for ACE-CYX bond Carlos Simmerling
- [AMBER] Loading RNA nucleotide (ADE) tleap error Rana Rehan Khalid
- Re: [AMBER] Lite Hash Rate and pmemd.cuda Ross Walker
- Re: [AMBER] Why is self-correlation with atomiccorr in cpptraj zero? Daniel Roe
- Re: [AMBER] Loading RNA nucleotide (ADE) tleap error David A Case
Friday, 6 August 2021
- Re: [AMBER] Missing mtkpp directory after installation of AmberTools21 Pengfei Li
Saturday, 7 August 2021
- [AMBER] How to set a replusive force between two drug molecules or two atoms. neildancer.sina.com
Sunday, 8 August 2021
- [AMBER] Amber20 installation, pip not installed in Miniconda Setyanto Md
Monday, 9 August 2021
- [AMBER] MCPB.py - ComplexWarning: Casting complex values to real discards the imaginary part Anthony Nash
- Re: [AMBER] Amber20 installation, pip not installed in Miniconda David A Case
- [AMBER] Developing Parameters for Bad Atom Types Matthew Guberman-Pfeffer
- [AMBER] tleap urea "[atom] does not have a type" Daniel Konstantinovsky
- [AMBER] EEE_INVALID_FLAG IEEE_OVERFLOW_FLAG IEEE_UNDERFLOW_FLAG IEEE_DENORMAL. Akinyemi Omoniyi
- Re: [AMBER] tleap urea "[atom] does not have a type" Hector A. Baldoni
- [AMBER] query about MD analysis Sadaf Rani
- Re: [AMBER] EEE_INVALID_FLAG IEEE_OVERFLOW_FLAG IEEE_UNDERFLOW_FLAG IEEE_DENORMAL. David A Case
- [AMBER] X-aligned.Box 刘保艳
- Re: [AMBER] X-aligned.Box Elvis A F Martis
Tuesday, 10 August 2021
- [AMBER] "An All-Atom Force Field for Metallocenes" Gustaf Olsson
- Re: [AMBER] query about MD analysis Clorice Reinhardt
- Re: [AMBER] "An All-Atom Force Field for Metallocenes" Gustaf Olsson
- [AMBER] Yet again, MCPB.py for a ferrocene terminated monomer. Gustaf Olsson
- [AMBER] Fwd: Lida Cheng
- [AMBER] Installation problem Lida Cheng
- Re: [AMBER] Installation problem David A Case
- [AMBER] Rodrigues' rotation about a specified vector Vaibhav Dixit
- Re: [AMBER] Rodrigues' rotation about a specified vector David A Case
Wednesday, 11 August 2021
- Re: [AMBER] Yet again, MCPB.py for a ferrocene terminated monomer. Gustaf Olsson
- Re: [AMBER] MCPB.py - ComplexWarning: Casting complex values to real discards the imaginary part Anthony Nash
- Re: [AMBER] X-aligned.Box Daniel Roe
- Re: [AMBER] Developing Parameters for Bad Atom Types Carlos Simmerling
- [AMBER] system preparation error Renato Araujo
- [AMBER] constant ph md Abhik Ghosh Moulick
- Re: [AMBER] Rodrigues' rotation about a specified vector Vaibhav Dixit
Thursday, 12 August 2021
- [AMBER] PCA and K-mean together scripting in CPPTRAJ Nisha Amarnath Jonniya
- Re: [AMBER] constant ph md David A Case
- Re: [AMBER] system preparation error David A Case
- Re: [AMBER] system preparation error Stephan Schott
- Re: [AMBER] system preparation error Renato Araujo
- Re: [AMBER] system preparation error Carlos Simmerling
- Re: [AMBER] PCA and K-mean together scripting in CPPTRAJ Christina Bergonzo
- Re: [AMBER] Yet again, MCPB.py for a ferrocene terminated monomer. Gustaf Olsson
- [AMBER] Installation Problem Lida Cheng
- [AMBER] CMake Error Rodrigo da Silva Bitzer
- [AMBER] Restraint weight in minimization Sadaf Rani
- Re: [AMBER] Installation Problem David A Case
- Re: [AMBER] CMake Error David A Case
- Re: [AMBER] Restraint weight in minimization Carlos Simmerling
- [AMBER] AMBER 18 and A100? Ilyas Yildirim
Friday, 13 August 2021
- [AMBER] Maximum coordination exceeded Gustaf Olsson
- Re: [AMBER] Maximum coordination exceeded Gustaf Olsson
- Re: [AMBER] Maximum coordination exceeded Gustaf Olsson
- Re: [AMBER] Maximum coordination exceeded Gustaf Olsson
- Re: [AMBER] Maximum coordination exceeded Gustaf Olsson
- Re: [AMBER] Maximum coordination exceeded Gustaf Olsson
- Re: [AMBER] PCA and K-mean together scripting in CPPTRAJ Nisha Amarnath Jonniya
- Re: [AMBER] Maximum coordination exceeded Carlos Simmerling
- Re: [AMBER] Maximum coordination exceeded Gustaf Olsson
- Re: [AMBER] Maximum coordination exceeded Gustaf Olsson
- Re: [AMBER] Maximum coordination exceeded David A Case
- Re: [AMBER] Maximum coordination exceeded Gustaf Olsson
- Re: [AMBER] Restraint weight in minimization Adrian Roitberg
- [AMBER] [Amber] Convert pqr to pdb Rohanizeidanlou, Sahar
- Re: [AMBER] [Amber] Convert pqr to pdb Daniel Roe
- [AMBER] Error open-mai Rodrigo da Silva Bitzer
- [AMBER] How to cap the residue/ nucleotide atoms Rana Rehan Khalid
Saturday, 14 August 2021
- Re: [AMBER] Error open-mai David A Case
- Re: [AMBER] How to cap the residue/ nucleotide atoms David A Case
- [AMBER] how to set distance restraints in amber Sadaf Rani
- Re: [AMBER] [Amber] Convert pqr to pdb Rohanizeidanlou, Sahar
Sunday, 15 August 2021
- Re: [AMBER] MCPB.py - ComplexWarning: Casting complex values to real discards the imaginary part Anthony Nash
- [AMBER] CUDA installation for use with AMBER20 James Kress
- Re: [AMBER] Rodrigues' rotation about a specified vector David A Case
Monday, 16 August 2021
- [AMBER] Adding distance restraint in amber Sadaf Rani
- [AMBER] Regarding standard deviation and SEM in hbond analysis Rajarshi Roy
- [AMBER] resp2.chg file is missing whilst processing 3rd stage of MCPB.py Anthony Nash
- Re: [AMBER] resp2.chg file is missing whilst processing 3rd stage of MCPB.py Aashish Bhatt
- Re: [AMBER] resp2.chg file is missing whilst processing 3rd stage of MCPB.py Anthony Nash
- Re: [AMBER] Adding distance restraint in amber David A Case
- Re: [AMBER] Adding distance restraint in amber Daniel Roe
- Re: [AMBER] Regarding standard deviation and SEM in hbond analysis Daniel Roe
- [AMBER] Positive value of electrostatic and negative value of EPB assawin daducale
Tuesday, 17 August 2021
- Re: [AMBER] Regarding standard deviation and SEM in hbond analysis Rajarshi Roy
- Re: [AMBER] Positive value of electrostatic and negative value of EPB David A Case
- [AMBER] Regarding filling missing residues in a DNA strand Sruthi Sudhakar
- [AMBER] Missing name.ncrst and name.nc files. Bruno Cramer
- Re: [AMBER] Missing name.ncrst and name.nc files. Carlos Simmerling
Wednesday, 18 August 2021
- Re: [AMBER] Missing name.ncrst and name.nc files. David A Case
- [AMBER] How to use parmed in Amber20 tools neildancer.sina.com
- Re: [AMBER] Regarding filling missing residues in a DNA strand David A Case
- Re: [AMBER] [Amber] Convert pqr to pdb Daniel Roe
- [AMBER] CPPTRAJ and data from PQR files Matthew Guberman-Pfeffer
- [AMBER] Combining MCPB.py results using tleap Anthony Nash
- Re: [AMBER] [UCE] Combining MCPB.py results using tleap Sarah Lefave
- Re: [AMBER] [UCE] Combining MCPB.py results using tleap Anthony Nash
Thursday, 19 August 2021
- [AMBER] Error 11 Paramfit Swisher, Justin S
- Re: [AMBER] [Amber] Convert pqr to pdb Rohanizeidanlou, Sahar
- [AMBER] Grumpy GROMBER over a ZeroDivisionError Matthew Guberman-Pfeffer
Friday, 20 August 2021
- [AMBER] MMGBSA_MPI for membrane-bound proteins Rafał Madaj
Saturday, 21 August 2021
- [AMBER] Restart interrupted sander.MPI calculation Bruno Cramer
Sunday, 22 August 2021
- Re: [AMBER] Restart interrupted sander.MPI calculation David A Case
- [AMBER] Grumpy GROMBER over a ZeroDivisionError Matthew Guberman-Pfeffer
- [AMBER] run_cmake with -DMPI=TRUE fails to produce MPI version of Amber20 James Kress
- [AMBER] Lone Pair Issue Li,Haoxi
- Re: [AMBER] run_cmake with -DMPI=TRUE fails to produce MPI version of Amber20 James Kress
- Re: [AMBER] run_cmake with -DMPI=TRUE fails to produce MPI version of Amber20 James Kress
- Re: [AMBER] run_cmake with -DMPI=TRUE fails to produce MPI version of Amber20 David A Case
- Re: [AMBER] run_cmake with -DMPI=TRUE fails to produce MPI version of Amber20 James Kress
- [AMBER] Question about thermodynamic integration. neildancer.sina.com
Monday, 23 August 2021
- Re: [AMBER] Amber parmeters for ACE-CYX bond Ali Saad Kusay
- Re: [AMBER] Grumpy GROMBER over a ZeroDivisionError David A Case
- [AMBER] Issue with MM/PBSA calculations on membrane system Gilberto Pereira
- Re: [AMBER] Question about thermodynamic integration. David A Case
- Re: [AMBER] Issue with MM/PBSA calculations on membrane system Ray Luo
- [AMBER] Building pmemd.cuda.MPI with NCCL support James Kress
- Re: [AMBER] Question about thermodynamic integration. neildancer
Tuesday, 24 August 2021
- [AMBER] Fwd: leap error for modified amino acid Ipsita Basu
- Re: [AMBER] Fwd: leap error for modified amino acid David A Case
- Re: [AMBER] Fwd: leap error for modified amino acid Ipsita Basu
Wednesday, 25 August 2021
- Re: [AMBER] Regarding filling missing residues in a DNA strand Sruthi Sudhakar
- Re: [AMBER] Regarding filling missing residues in a DNA strand Carlos Simmerling
- Re: [AMBER] Grumpy GROMBER over a ZeroDivisionError Jason Swails
- Re: [AMBER] Error 11 Paramfit Swisher, Justin S
- [AMBER] Issue running sander Vento, Gabby
- Re: [AMBER] Issue running sander Clorice Reinhardt
Thursday, 26 August 2021
- [AMBER] iron-sulfur clusters parameters Patsch David (patc)
- Re: [AMBER] Error 11 Paramfit Robin Betz
- [AMBER] Suggestions for Mn3O4 Subhadip Basu
- [AMBER] Unit cell size has changed in trajcetory Sadaf Rani
Friday, 27 August 2021
- Re: [AMBER] Unit cell size has changed in trajcetory Daniel Roe
- Re: [AMBER] iron-sulfur clusters parameters David A Case
- Re: [AMBER] iron-sulfur clusters parameters Gerald Monard
Saturday, 28 August 2021
- Re: [AMBER] How to cap the residue/ nucleotide atoms Rana Rehan Khalid
- Re: [AMBER] How to cap the residue/ nucleotide atoms David A Case
Sunday, 29 August 2021
- [AMBER] descrepancy in net charge - TI output Delwakkada Liyanage, Senal Dinuka
Monday, 30 August 2021
- Re: [AMBER] descrepancy in net charge - TI output David A Case
- Re: [AMBER] descrepancy in net charge - TI output Delwakkada Liyanage, Senal Dinuka
- Re: [AMBER] How to get code modifications into AmberTools Tharrington, Arnold
- Re: [AMBER] How to get code modifications into AmberTools David A Case
- Re: [AMBER] descrepancy in net charge - TI output David A Case
- [AMBER] An question about Tutorial wangwei1669
- Re: [AMBER] {SPAM?} An question about Tutorial Matthew Guberman-Pfeffer
- [AMBER] Need help with MMPBSA-per residue decomp Yen Nguyen
- [AMBER] The paramters of TI neildancer.sina.com
Tuesday, 31 August 2021
- Re: [AMBER] An question about Tutorial Carlos Simmerling
- Re: [AMBER] Unit cell size has changed in trajcetory Daniel Roe
- Re: [AMBER] Error 11 Paramfit Dr. Anselm Horn
- Re: [AMBER] descrepancy in net charge - TI output Delwakkada Liyanage, Senal Dinuka

Last message date: Tue Aug 31 2021 - 15:30:02 PDT
Archived on: Mon Apr 22 2024 - 05:56:00 PDT

Amber Archive Aug 2021 by date