Amber Archive Aug 2018: by date

Wednesday, 1 August 2018
- [AMBER] Constant pH simulation in explicit solvent Nikolay N. Kuzmich
- Re: [AMBER] Constant pH simulation in explicit solvent Eric Lang
- [AMBER] Eigenvalues from PCA in cpptraj Adam Jo Elatico
- [AMBER] asking about PBRadii in MMPBSA an other else Setyanto Md
- [AMBER] Multiple PDB files to a MDCRD file Alechania Misturini
- Re: [AMBER] MCBP force constants Seibold, Steve Allan
- Re: [AMBER] Eigenvalues from PCA in cpptraj Daniel Roe
- Re: [AMBER] Multiple PDB files to a MDCRD file Daniel Roe
- Re: [AMBER] Multiple PDB files to a MDCRD file Charles-Alexandre Mattelaer
- Re: [AMBER] Multiple PDB files to a MDCRD file Daniel Roe
- Re: [AMBER] Eigenvalues from PCA in cpptraj Adam Jo Elatico
- Re: [AMBER] Eigenvalues from PCA in cpptraj Daniel Roe
- Re: [AMBER] Multiple PDB files to a MDCRD file Alechania Misturini
- [AMBER] Fwd: Issue with imploding structure during heating and equilibration David Stevens
- [AMBER] GPUs Alexandra Carvalho
- Re: [AMBER] Possible bug on addLJType command of Parmed Jason Swails
- Re: [AMBER] very slow implicit simulation on GPU!!! Jason Swails
- Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM Tyler Luchko (Lists)
- Re: [AMBER] GPUs David Cerutti
- [AMBER] Reproduce part of AMBER trajectory Supriyo Bhattacharya
- Re: [AMBER] Multiple PDB files to a MDCRD file David A Case
Thursday, 2 August 2018
- [AMBER] Calculate protein energy from simulation trajectory Adam Jo Elatico
- Re: [AMBER] Constant pH simulation in explicit solvent Nikolay N. Kuzmich
- Re: [AMBER] Fwd: Issue with imploding structure during heating and equilibration Carlos Simmerling
- [AMBER] Velocity Format in AMBER BLEY Michael
- [AMBER] System density decrease during accelerated MD: why? Nikolay N. Kuzmich
- Re: [AMBER] QM/MM link atoms emanuele falbo
- Re: [AMBER] Multiple PDB files to a MDCRD file Alechania Misturini
- Re: [AMBER] Multiple PDB files to a MDCRD file Alechania Misturini
- Re: [AMBER] QM/MM link atoms Gustavo Seabra
- [AMBER] Free energy landscape on principal components Adam Jo Elatico
- Re: [AMBER] Velocity Format in AMBER David A Case
- Re: [AMBER] QM/MM link atoms Goetz, Andreas
- Re: [AMBER] Possible bug on addLJType command of Parmed Matias Machado
- Re: [AMBER] QM/MM link atoms James Kress
- Re: [AMBER] QM/MM link atoms Goetz, Andreas
- [AMBER] MCPB.py with G09 rev. B.01 Jinfeng Chen
Friday, 3 August 2018
- [AMBER] COM pulling in direction Meng Wu
- [AMBER] Amber16 Installation error Sushi Shilpa
- Re: [AMBER] eCheminfo Oxford 3-7 Sep., Training and Innovation Course in Drug Design, bursary and early-bird deadline approaching quickly Thomas Exner
- Re: [AMBER] Amber16 Installation error Matias Machado
- Re: [AMBER] Amber16 Installation error Sushi Shilpa
- Re: [AMBER] Amber16 Installation error Matias Machado
- Re: [AMBER] Amber16 Installation error Matias Machado
- Re: [AMBER] Amber16 Installation error Sushi Shilpa
- Re: [AMBER] Amber16 Installation error Sushi Shilpa
- [AMBER] Error for Amber16 and Amber tools 17 installation maryam azimzadehirani
- [AMBER] Solute-solvent hydrogen bond lifetime ATUL KUMAR
- [AMBER] error_antechamber (QMMM: ERROR!) Atila Petrosian
- [AMBER] Change in boxlength during memebrane simulation somdev pahari
- Re: [AMBER] Change in boxlength during memebrane simulation David Cerutti
- Re: [AMBER] error_antechamber (QMMM: ERROR!) Gustavo Seabra
- [AMBER] error_antechamber (QMMM: ERROR!) Atila Petrosian
- Re: [AMBER] Change in boxlength during memebrane simulation somdev pahari
- Re: [AMBER] Reading grid data from standard datafile I Lőrincz
- Re: [AMBER] error_antechamber (QMMM: ERROR!) Goetz, Andreas
- [AMBER] RES: error_antechamber (QMMM: ERROR!) gustavo.seabra.gmail.com
- Re: [AMBER] RES: error_antechamber (QMMM: ERROR!) Atila Petrosian
- Re: [AMBER] Error for Amber16 and Amber tools 17 installation Josh Berryman
- Re: [AMBER] Change in boxlength during memebrane simulation Sally Pias
- Re: [AMBER] Change in boxlength during memebrane simulation David Cerutti
- Re: [AMBER] Change in boxlength during memebrane simulation Chris Neale
- Re: [AMBER] Change in boxlength during memebrane simulation David Cerutti
- Re: [AMBER] Amber16 Installation error Sushi Shilpa
Saturday, 4 August 2018
- Re: [AMBER] COM pulling in direction Meng Wu
- Re: [AMBER] Error for Amber16 and Amber tools 17 installation maryam azimzadehirani
- Re: [AMBER] Error for Amber16 and Amber tools 17 installation David A Case
Sunday, 5 August 2018
- Re: [AMBER] Error for Amber16 and Amber tools 17 installation Kevin Keane (USD)
- [AMBER] counterions_automatic Antonio Amber Carlesso
- [AMBER] Adding box dimension Simon Kit Sang Chu
- Re: [AMBER] counterions_automatic Matias Machado
Monday, 6 August 2018
- [AMBER] Atom Types for carbons with unsaturated bond Vijay Achari
- [AMBER] Parameters for non-standard residues Anuja Ware
- Re: [AMBER] Parameters for non-standard residues Zhonghua Xia
- Re: [AMBER] Adding box dimension David A Case
- Re: [AMBER] Parameters for non-standard residues David A Case
- Re: [AMBER] Adding box dimension Simon Kit Sang Chu
- Re: [AMBER] Parameters for non-standard residues Junmei Wang
- Re: [AMBER] Solute-solvent hydrogen bond lifetime Daniel Roe
- [AMBER] RDCs in pmemd? Thomas Pochapsky
- Re: [AMBER] Adding box dimension David Cerutti
- Re: [AMBER] Running a small minimization with amber 16 package Debarati DasGupta
- Re: [AMBER] Running a small minimization with amber 16 package Scott Brozell
- [AMBER] COM pulling in direction Meng Wu
Tuesday, 7 August 2018
- Re: [AMBER] Solute-solvent hydrogen bond lifetime ATUL KUMAR
- Re: [AMBER] COM pulling in direction Feng Pan
- Re: [AMBER] Error for Amber16 and Amber tools 17 installation maryam azimzadehirani
- [AMBER] .frcmod_file_generation Antonio Amber Carlesso
- Re: [AMBER] counterions_automatic Antonio Amber Carlesso
- [AMBER] max# cpu's for sander, specify which gpu runs a job David Christopher Schröder
- Re: [AMBER] MCPB.py with G09 rev. B.01 Pengfei Li
- Re: [AMBER] .frcmod_file_generation David A Case
- Re: [AMBER] max# cpu's for sander, specify which gpu runs a job David A Case
- [AMBER] Restraints on a system Debarati DasGupta
- Re: [AMBER] COM pulling in direction Meng Wu
- Re: [AMBER] .frcmod_file_generation Antonio Amber Carlesso
Wednesday, 8 August 2018
- [AMBER] problem with amber 16 giovanna rogati
- [AMBER] number of interconversions from free energy landscape (FEL) plot Chetna Tyagi
- [AMBER] checkmolecule.c John L. Kulp, Jr.
- [AMBER] Speeding up sqm, PM6 vs AM1 for am1-bcc John L. Kulp, Jr.
- Re: [AMBER] problem with amber 16 David A Case
- [AMBER] Amber18 on NVIDIA Quadro Cards mish
- Re: [AMBER] Amber18 on NVIDIA Quadro Cards Ross Walker
- Re: [AMBER] Amber18 on NVIDIA Quadro Cards James Kress
- Re: [AMBER] Amber18 on NVIDIA Quadro Cards David Cerutti
- Re: [AMBER] checkmolecule.c David A Case
- Re: [AMBER] Amber18 on NVIDIA Quadro Cards Ross Walker
- Re: [AMBER] Amber18 on NVIDIA Quadro Cards Ross Walker
- Re: [AMBER] checkmolecule.c David A Case
- Re: [AMBER] Speeding up sqm, PM6 vs AM1 for am1-bcc David A Case
- Re: [AMBER] Amber18 on NVIDIA Quadro Cards James Kress
- [AMBER] Erreneous PMF Stefan Ivanov
Thursday, 9 August 2018
- [AMBER] how to install PTRAJ and CPPTRAJ Subrata Paul
- Re: [AMBER] how to install PTRAJ and CPPTRAJ Rodrigo Galindo-Murillo
- Re: [AMBER] how to install PTRAJ and CPPTRAJ Subrata Paul
- Re: [AMBER] Amber18 on NVIDIA Quadro Cards mish
- Re: [AMBER] Amber18 on NVIDIA Quadro Cards malkeet singh Bahia
- Re: [AMBER] Amber18 on NVIDIA Quadro Cards mish
- [AMBER] Cpptraj not working Subrata Paul
- [AMBER] mistake in source-code in egb.F90 Johannes Kalliauer
- Re: [AMBER] Cpptraj not working Marcelo Andrade Chagas
- Re: [AMBER] Erreneous PMF Dickson, Callum
- Re: [AMBER] how to install PTRAJ and CPPTRAJ Daniel Roe
- [AMBER] PrmtopError: Inconsistent charge definition for atom Santanu Santra
- Re: [AMBER] Amber18 on NVIDIA Quadro Cards Ross Walker
- Re: [AMBER] Amber18 on NVIDIA Quadro Cards Ross Walker
- [AMBER] miRNA-mRNA structure / NAB Atila Petrosian
- [AMBER] cpptraj / ambpdb only selected atoms / residues Simon Kit Sang Chu
- Re: [AMBER] cpptraj / ambpdb only selected atoms / residues Daniel Roe
- Re: [AMBER] Cpptraj not working Subrata Paul
- Re: [AMBER] Cpptraj not working Daniel Roe
- Re: [AMBER] cpptraj / ambpdb only selected atoms / residues Simon Kit Sang Chu
- Re: [AMBER] miRNA-mRNA structure / NAB David A Case
- Re: [AMBER] cpptraj / ambpdb only selected atoms / residues Daniel Roe
- [AMBER] X-mer analysis or statistics ? Marek Maly
- Re: [AMBER] Erreneous PMF Stefan Ivanov
Friday, 10 August 2018
- [AMBER] Amber Installation: MPI Error Aravind Ravichandran
- Re: [AMBER] Amber18 on NVIDIA Quadro Cards mish
- [AMBER] command not found Sushi Shilpa
- [AMBER] How to use filter command to find the structures of high density during PCA analysis? Markowska
- Re: [AMBER] Amber Installation: MPI Error David A Case
- Re: [AMBER] command not found David A Case
- Re: [AMBER] Erreneous PMF Dickson, Callum
- [AMBER] Research Programmers Positions Available João Ribeiro
- Re: [AMBER] Change in boxlength during memebrane simulation Sally Pias
- Re: [AMBER] Erreneous PMF Stefan Ivanov
Saturday, 11 August 2018
- [AMBER] sander.MPI running on only one node Leena Aggarwal
- Re: [AMBER] sander.MPI running on only one node Matias Machado
- Re: [AMBER] Restraints on a system Matias Machado
- Re: [AMBER] Restraints on a system Matias Machado
- [AMBER] # of Coordinates Mismatch in PCA Robert Molt
Sunday, 12 August 2018
- [AMBER] Warning: DISABLING BOX in topology '<name>.pdb'! Dmitry Suplatov
- [AMBER] alkyl chain unsaturated bond Vijay Achari
- [AMBER] MMPBSA.PY 龚乾坤
- Re: [AMBER] # of Coordinates Mismatch in PCA Kenneth Huang
Monday, 13 August 2018
- [AMBER] Can I calculate the domain-domain interaction energy using the MMPBSA.py tool? maryam azimzadehirani
- Re: [AMBER] alkyl chain unsaturated bond Dickson, Callum
- [AMBER] amber18 and amazon aws Luca Codutti
- Re: [AMBER] amber18 and amazon aws David Cerutti
- Re: [AMBER] # of Coordinates Mismatch in PCA Robert Molt
Tuesday, 14 August 2018
- Re: [AMBER] max# cpu's for sander, specify which gpu runs a job David Christopher Schröder
- [AMBER] A question about tleap 龚乾坤
- [AMBER] tleap_protein_preparation_general_rule Antonio Amber Carlesso
- Re: [AMBER] A question about tleap Nisha Amarnath Jonniya
- [AMBER] QM/MM Thermodynamic Integration emanuele
- Re: [AMBER] tleap_protein_preparation_general_rule David A Case
- Re: [AMBER] QM/MM Thermodynamic Integration David A Case
- Re: [AMBER] RDCs in pmemd? David A Case
- Re: [AMBER] QM/MM Thermodynamic Integration James Kress
- Re: [AMBER] tleap_protein_preparation_general_rule Antonio Amber Carlesso
- Re: [AMBER] # of Coordinates Mismatch in PCA Kenneth Huang
- Re: [AMBER] tleap_protein_preparation_general_rule Matias Machado
- Re: [AMBER] tleap_protein_preparation_general_rule Antonio Amber Carlesso
- Re: [AMBER] # of Coordinates Mismatch in PCA Jason Swails
- Re: [AMBER] # of Coordinates Mismatch in PCA Robert Molt
- Re: [AMBER] MMPBSA.PY Jason Swails
- Re: [AMBER] PrmtopError: Inconsistent charge definition for atom Jason Swails
- [AMBER] Problem with QMMM with Amber/Gaussian interface. Sadra Aghajani
- Re: [AMBER] Problem with QMMM with Amber/Gaussian interface. Goetz, Andreas
Wednesday, 15 August 2018
- [AMBER] HOW to type a free CYS molecule MinYuan
- Re: [AMBER] HOW to type a free CYS molecule David A Case
- Re: [AMBER] checkmolecule.c Scott Brozell
- Re: [AMBER] HOW to type a free CYS molecule Matias Machado
- Re: [AMBER] HOW to type a free CYS molecule MinYuan
- Re: [AMBER] HOW to type a free CYS molecule MinYuan
- Re: [AMBER] problem with amber 16 giovanna rogati
Thursday, 16 August 2018
- [AMBER] Multiple trajectory analysis with CPPTRAJ and getting output for each of them separately Luka Bilić
- [AMBER] implement_revised_RNA_force_field_general rule? Antonio Amber Carlesso
- [AMBER] cpptraj segmentation fault when using avgout in cluster Charo del Genio
- Re: [AMBER] alkyl chain unsaturated bond Vijay Achari
- Re: [AMBER] checkmolecule.c John Kulp
- Re: [AMBER] alkyl chain unsaturated bond Dickson, Callum
- [AMBER] AM1BCC challenge with atomic types recognition and convertion of .ac to .mol2 Sergey Samsonov
- Re: [AMBER] implement_revised_RNA_force_field_general rule? Matias Machado
- Re: [AMBER] AM1BCC challenge with atomic types recognition and convertion of .ac to .mol2 David A Case
- Re: [AMBER] implement_revised_RNA_force_field_general rule? David A Case
Friday, 17 August 2018
- Re: [AMBER] AM1BCC challenge with atomic types recognition and convertion of .ac to .mol2 Sergey Samsonov
- [AMBER] About calculating entropy in MM_PB/GBSA using mm_pbsa.pl 龚乾坤
- [AMBER] MMPBSA.PY 龚乾坤
- [AMBER] Where is the source code adjusting the size of the periodic boundary condition box in NPT ensemble ? jinfeng liu
- [AMBER] Mutation Free Energy hosein geraili
- [AMBER] TLEAP script Keiran Corbett
- Re: [AMBER] About calculating entropy in MM_PB/GBSA using mm_pbsa.pl David A Case
- Re: [AMBER] The instructions of the .out file Zhonghua Xia
- Re: [AMBER] Mutation Free Energy David A Case
- Re: [AMBER] TLEAP script David A Case
- Re: [AMBER] Where is the source code adjusting the size of the periodic boundary condition box in NPT ensemble ? David A Case
- Re: [AMBER] Where is the source code adjusting the size of the periodic boundary condition box in NPT ensemble ? jinfeng liu
- [AMBER] Error in Running heating in GPU enabled AMBER kuldeep singh
- [AMBER] SCF convergence problems and write density matrix Anaid Flores
- Re: [AMBER] Error in Running heating in GPU enabled AMBER David A Case
Saturday, 18 August 2018
- Re: [AMBER] SCF convergence problems and write density matrix Gerald Monard
- [AMBER] update to Amber18's pmemd.cuda code David A Case
- [AMBER] How to convert QM parameters to AMBER force field parameters MinYuan
- Re: [AMBER] SCF convergence problems and write density matrix Sadra Aghajani
- Re: [AMBER] implement_revised_RNA_force_field_general rule? Antonio Amber Carlesso
- Re: [AMBER] implement_revised_RNA_force_field_general rule? David A Case
Sunday, 19 August 2018
- Re: [AMBER] implement_revised_RNA_force_field_general rule? Antonio Amber Carlesso
- [AMBER] cpptraj and ptraj not installed Subrata Paul
- Re: [AMBER] cpptraj and ptraj not installed Hai Nguyen
- Re: [AMBER] SCF convergence problems and write density matrix Anaid Flores
Monday, 20 August 2018
- Re: [AMBER] TLEAP script Keiran Corbett
- [AMBER] Scripting Bash to tleap Keiran Corbett
- Re: [AMBER] Scripting Bash to tleap David A Case
- Re: [AMBER] Scripting Bash to tleap Wesley Michael Botello-Smith
- Re: [AMBER] Scripting Bash to tleap Wesley Michael Botello-Smith
- [AMBER] metalParm2.xml or metalParm.xml Seibold, Steve Allan
- Re: [AMBER] Multiple trajectory analysis with CPPTRAJ and getting output for each of them separately Daniel Roe
- Re: [AMBER] Warning: DISABLING BOX in topology '<name>.pdb'! Daniel Roe
- [AMBER] How to calculate SASA for an arbitrary solvent Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] # of Coordinates Mismatch in PCA Robert Molt
- Re: [AMBER] # of Coordinates Mismatch in PCA Jason Swails
- [AMBER] Umbrella sampling run error Rakesh Srivastava
- Re: [AMBER] Umbrella sampling run error Bill Ross
- Re: [AMBER] Umbrella sampling run error Rakesh Srivastava
Tuesday, 21 August 2018
- [AMBER] ASMD for decrease in distance between ligand and catalytic site sangita kachhap
- Re: [AMBER] # of Coordinates Mismatch in PCA Daniel Roe
- Re: [AMBER] cpptraj segmentation fault when using avgout in cluster Daniel Roe
- Re: [AMBER] # of Coordinates Mismatch in PCA Robert Molt
- Re: [AMBER] # of Coordinates Mismatch in PCA Daniel Roe
- Re: [AMBER] # of Coordinates Mismatch in PCA Robert Molt
- Re: [AMBER] cpptraj segmentation fault when using avgout in cluster Charo del Genio
- Re: [AMBER] # of Coordinates Mismatch in PCA Jason Swails
- Re: [AMBER] ASMD for decrease in distance between ligand and catalytic site Feng Pan
Wednesday, 22 August 2018
- [AMBER] H-bond between the substrate molecule and protein in the MD traj Meng Wu
- Re: [AMBER] amber18 and amazon aws Luca Codutti
- Re: [AMBER] ASMD for decrease in distance between ligand and catalytic site sangita kachhap
- [AMBER] Umbrella sampling rst file error M RCC
- [AMBER] restraintmask input setup Lod King
- [AMBER] Need help regarding Lifetime Curve of Hydrogen bond analysis Bharat Manna
Thursday, 23 August 2018
- [AMBER] Problems with constant pH production step Helena Damtoft Tjørnelund
- Re: [AMBER] Problems with constant pH production step Bill Ross
- Re: [AMBER] Umbrella sampling rst file error David A Case
- Re: [AMBER] restraintmask input setup David A Case
- Re: [AMBER] Problems with constant pH production step Jason Swails
- Re: [AMBER] Problems with constant pH production step Helena Damtoft Tjørnelund
Friday, 24 August 2018
- Re: [AMBER] Problems with constant pH production step Cruzeiro,Vinicius Wilian D
- Re: [AMBER] Problems with constant pH production step Helena Damtoft Tjørnelund
- Re: [AMBER] Problems with constant pH production step Cruzeiro,Vinicius Wilian D
- [AMBER] Need help regarding calculation of Coordination number from RDF Profile Bharat Manna
- Re: [AMBER] Problems with constant pH production step Jason Swails
- Re: [AMBER] Need help regarding calculation of Coordination number from RDF Profile Daniel Roe
- [AMBER] Thank you Tai Tze Hong
Saturday, 25 August 2018
- [AMBER] Amber18 error: an illegal memory access was encountered launching kernel kNLSkinTest 李耀
- Re: [AMBER] Amber18 error: an illegal memory access was encountered launching kernel kNLSkinTest accuratefreeenergy.gmail.com
- [AMBER] NCSU_SMD for protein-ligand complex pulling M RCC
- Re: [AMBER] NCSU_SMD for protein-ligand complex pulling Feng Pan
Sunday, 26 August 2018
- Re: [AMBER] Amber18 error: an illegal memory access was encountered launching kernel kNLSkinTest David A Case
- [AMBER] MG Coordination System: Nonbonded Cationic Dummy Model Aravind Ravichandran
- [AMBER] GIST calculation M RCC
Monday, 27 August 2018
- [AMBER] Amber 18 targeted MD errorin input::atommask.f::pop_evalstack stack underflow 李耀
- Re: [AMBER] MG Coordination System: Nonbonded Cationic Dummy Model Qinghua Liao
- [AMBER] Error: System density has likely changed M RCC
- Re: [AMBER] Error: System density has likely changed David A Case
Sunday, 26 August 2018
- [AMBER] A part of protein molecule moving out of the box Sanjib Paul
Monday, 27 August 2018
- Re: [AMBER] A part of protein molecule moving out of the box Carlos Simmerling
- [AMBER] Best Methods Leon Hardy
- Re: [AMBER] Thank you elias_christoforides
- [AMBER] Are there any forcefield present of bio-organic polyphosphate in AMBER ?? Saikat Pal
- Re: [AMBER] Are there any forcefield present of bio-organic polyphosphate in AMBER ?? Alechania Misturini
- Re: [AMBER] Best Methods Alechania Misturini
- Re: [AMBER] Amber 18 targeted MD errorin input::atommask.f::pop_evalstack stack underflow Daniel Roe
- Re: [AMBER] Error: System density has likely changed David Cerutti
- Re: [AMBER] Error: System density has likely changed David Cerutti
- [AMBER] Amber16 installation error Renato Araujo
- Re: [AMBER] Amber16 installation error Bill Ross
- Re: [AMBER] Amber16 installation error Renato Araujo
- Re: [AMBER] Amber16 installation error Renato Araujo
- Re: [AMBER] Amber16 installation error David A Case
Tuesday, 28 August 2018
- [AMBER] Protein_ligand_preparation_general_rule Antonio Amber Carlesso
- Re: [AMBER] Protein_ligand_preparation_general_rule Keiran Corbett
- Re: [AMBER] GIST calculation Steven Ramsey
- Re: [AMBER] GIST calculation Daniel Roe
- [AMBER] R.E.D. Server is down Anthony Bogetti
- Re: [AMBER] Protein_ligand_preparation_general_rule David A Case
Wednesday, 29 August 2018
- Re: [AMBER] Protein_ligand_preparation_general_rule Antonio Amber Carlesso
- [AMBER] I want to calculate electrostatic and van der Waals energy Saikat Pal
- [AMBER] How to define the speed of pulling ligand in SMD? M RCC
- [AMBER] RED SERVER DOWN Corinn Durham
- [AMBER] The R.E.D. server is down Bellesis, Andrew G
- [AMBER] Heating error in complex sandeep singh
- [AMBER] How to use cpptraj to wrap protein Yang, Tianyi
Thursday, 30 August 2018
- [AMBER] Steered molecular dynamics..... pulling force is not decreasing M RCC
- [AMBER] CPPTRAJ issues parsing NETCDF RST file Gustaf Olsson
- Re: [AMBER] CPPTRAJ issues parsing NETCDF RST file Daniel Roe
- Re: [AMBER] Heating error in complex David A Case
- Re: [AMBER] How to use cpptraj to wrap protein Daniel Roe
- Re: [AMBER] Need help regarding Lifetime Curve of Hydrogen bond analysis Daniel Roe
- Re: [AMBER] H-bond between the substrate molecule and protein in the MD traj Daniel Roe
- Re: [AMBER] CPPTRAJ issues parsing NETCDF RST file Gustaf Olsson
- [AMBER] Normal mode calculation on a truncated system Marko Tomin
- Re: [AMBER] CPPTRAJ issues parsing NETCDF RST file Daniel Roe
- [AMBER] minimization restrain in Qm-mm/MD Thakur, Abhishek
- Re: [AMBER] minimization restrain in Qm-mm/MD Szymon Żaczek
- Re: [AMBER] Heating error in complex sandeep singh
- Re: [AMBER] CPPTRAJ issues parsing NETCDF RST file Gustaf Olsson
Friday, 31 August 2018
- Re: [AMBER] Heating error in complex David A Case
- [AMBER] Distance HH TIP3P David Sáez
- Re: [AMBER] How to use cpptraj to wrap protein Yang, Tianyi
- Re: [AMBER] Steered molecular dynamics..... pulling force is not decreasing Feng Pan
- Re: [AMBER] How to use cpptraj to wrap protein Daniel Roe

Last message date: Fri Aug 31 2018 - 17:00:02 PDT
Archived on: Fri Oct 31 2025 - 05:55:41 PDT

Amber Archive Aug 2018 by date