Amber Archive Jan 2019: by date

Monday, 31 December 2018
- Re: [AMBER] Obtaining necessary *.top for MMPBSA.py Elvis Martis
Tuesday, 1 January 2019
- [AMBER] orca failure in mdgx: QM grid file not found Anthony Bogetti
- [AMBER] error with HEM parm Mohammad Salem
Wednesday, 2 January 2019
- Re: [AMBER] error with HEM parm David A Case
- [AMBER] Understanding Distance Restraint Ara R
- Re: [AMBER] error with HEM parm Matthew Fisher
- [AMBER] Calculated dipole moment in AMBER Xiaocong Wang
- Re: [AMBER] Understanding Distance Restraint Charles Lin
- Re: [AMBER] Calculated dipole moment in AMBER Daniel Roe
- [AMBER] Amber Restraint output from Kung, Ryan
- [AMBER] DMF Arkajyoti Sengupta
- [AMBER] Error with mdnab from amberlite Sundar
- Re: [AMBER] Calculated dipole moment in AMBER Xiaocong Wang
- Re: [AMBER] DMF Thomas Cheatham
- Re: [AMBER] Calculated dipole moment in AMBER Fulbabu Sk
Thursday, 3 January 2019
- Re: [AMBER] Understanding Distance Restraint Stephan Schott
- Re: [AMBER] Calculated dipole moment in AMBER Daniel Roe
- Re: [AMBER-Developers] [AMBER] Error with mdnab from amberlite David A Case
- Re: [AMBER] Testing AMBER16 installation in parallel; possible bug in testing scripts Bellesis, Andrew G
- Re: [AMBER] Literature about magnesium ion parameters in tutorial A8 Zuo, Zhicheng
- Re: [AMBER] Calculated dipole moment in AMBER Fulbabu Sk
- [AMBER] Zeolite simulations Sundar
Friday, 4 January 2019
- Re: [AMBER] Literature about magnesium ion parameters in tutorial A8 Mauricio Esguerra
- Re: [AMBER] MMPBSA.py error Pratul Agarwal
- [AMBER] CUDA and Restraint Error Kung, Ryan
- Re: [AMBER] Error with mdnab from amberlite Sundar
Saturday, 5 January 2019
- Re: [AMBER] CUDA and Restraint Error David Case
- Re: [AMBER] CUDA and Restraint Error Stephan Schott
- Re: [AMBER] CUDA and Restraint Error Pratul Agarwal
- Re: [AMBER] CUDA and Restraint Error Mehreen Ghufran
- [AMBER] Si and Al parameters Sundar
- [AMBER] QM/MM-GBSA results Sundar
Sunday, 6 January 2019
- [AMBER] RMSF in amber Akshay Prabhakant
- Re: [AMBER] RMSF in amber Elvis Martis
Monday, 7 January 2019
- Re: [AMBER] RMSF in amber Daniel Roe
- [AMBER] Amber installation Yazan Haddad
- [AMBER] average mulliken charges Thakur, Abhishek
- Re: [AMBER] CUDA and Restraint Error Daniel Roe
- [AMBER] Problem with AMP atom separating in equilibration Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] RMSF in amber Elvis Martis
- Re: [AMBER] Amber installation Yazan Haddad
Tuesday, 8 January 2019
- [AMBER] Clipping radius in AddToBox Lucas Bandeira
- Re: [AMBER] Amber installation David A Case
- Re: [AMBER] Problem with AMP atom separating in equilibration David A Case
- Re: [AMBER] Clipping radius in AddToBox David Cerutti
- Re: [AMBER] Clipping radius in AddToBox David A Case
- Re: [AMBER] Clipping radius in AddToBox Lucas Bandeira
- [AMBER] "vlimit exceeded" in NVT simulation Lucas Bandeira
- Re: [AMBER] Clipping radius in AddToBox David Cerutti
- Re: [AMBER] "vlimit exceeded" in NVT simulation Pratul Agarwal
- Re: [AMBER] Amber installation Yazan Haddad
- [AMBER] makeDIST_RST Sundar
Wednesday, 9 January 2019
- [AMBER] steered md at constant force Batuhan Kav
- [AMBER] Cpptraj: std::bad_alloc error Nikolay N. Kuzmich
- [AMBER] How to load and visualize large trajectories? Chetna Tyagi
- Re: [AMBER] How to load and visualize large trajectories? Mehreen Ghufran
- Re: [AMBER] How to load and visualize large trajectories? Qinghua Liao
- Re: [AMBER] How to load and visualize large trajectories? Chetna Tyagi
- Re: [AMBER] How to load and visualize large trajectories? Chetna Tyagi
- Re: [AMBER] Cpptraj: std::bad_alloc error Pratul Agarwal
- Re: [AMBER] makeDIST_RST David A Case
- Re: [AMBER] Cpptraj: std::bad_alloc error Daniel Roe
- Re: [AMBER] How to load and visualize large trajectories? Daniel Roe
- Re: [AMBER] How to load and visualize large trajectories? Chetna Tyagi
- Re: [AMBER] Cpptraj: std::bad_alloc error Pratul Agarwal
- Re: [AMBER] makeDIST_RST Sundar
- [AMBER] TMD and pmemd Sundar
- Re: [AMBER] TMD and pmemd Wesley Michael Botello-Smith
Thursday, 10 January 2019
- Re: [AMBER] Cpptraj: std::bad_alloc error Nikolay N. Kuzmich
- Re: [AMBER] MCPB.py Modelling Question Pengfei Li
- Re: [AMBER] Zeolite simulations Pengfei Li
- [AMBER] Virtual Spin Labels in Amber Kari Gaalswyk
- [AMBER] MMPBSA.py- bad atom type "I" Subha Kalyaanamoorthy
- [AMBER] Installation error on cray machine Sundar
- [AMBER] NO and CO parameters from Antechamber Markowska
- Re: [AMBER] steered md at constant force Jason Swails
- [AMBER] Amber energy minimization and the energy unit Vasantha Kumar
Friday, 11 January 2019
- [AMBER] Problems with cutoff (?) Margarita I. Bernal-Uruchurtu
- [AMBER] reweighting aMD Núbia Prates
- Re: [AMBER] Amber energy minimization and the energy unit Pratul Agarwal
- [AMBER] "make test" 1 errors occur changseo park
- Re: [AMBER] NO and CO parameters from Antechamber David A Case
- Re: [AMBER] Installation error on cray machine Daniel Roe
- [AMBER] Constant external force in the given space zone ? Thermostat working just on selected part of simulated system ? Marek Maly
- [AMBER] TMD reporting force profile Sundar
- Re: [AMBER] Installation error on cray machine Sundar
- [AMBER] Modifying mdread2.F90 for bad atom type: "I" MMPBSA error Subha Kalyaanamoorthy
- Re: [AMBER] Installation error on cray machine Daniel Roe
- [AMBER] gpu_shuttle_post_data can't work in the implicit solvent 张浩淼
Saturday, 12 January 2019
- Re: [AMBER] gpu_shuttle_post_data can't work in the implicit solvent David Cerutti
- Re: [AMBER] Problems with cutoff (?) David Case
- Re: [AMBER] "make test" 1 errors occur David Case
- Re: [AMBER] Virtual Spin Labels in Amber David Case
Sunday, 13 January 2019
- [AMBER] DMF Arkajyoti Sengupta
- [AMBER] calculating am1-bcc charges from user generated mulliken charges Braden Kelly
- Re: [AMBER] calculating am1-bcc charges from user generated mulliken charges Braden Kelly
Monday, 14 January 2019
- [AMBER] Using Distance Restraints in TMD Aravind R
- Re: [AMBER] Zeolite simulations Sundar
- [AMBER] mutation using pdb4amber Sundar
- [AMBER] RMSD of independent trajectories using cpptraj Hunter Wilson
- Re: [AMBER] mutation using pdb4amber Hai Nguyen
- Re: [AMBER] RMSD of independent trajectories using cpptraj Daniel Roe
- [AMBER] Metal center molecule gaohanlu
Tuesday, 15 January 2019
- Re: [AMBER] "make test" 1 errors occur changseo park
- Re: [AMBER] Metal center molecule Saikat Pal
- Re: [AMBER] RMSD of independent trajectories using cpptraj Hunter Wilson
- Re: [AMBER] RMSD of independent trajectories using cpptraj Daniel Roe
- [AMBER] Autoimage command not working Martín Pettinati
- Re: [AMBER] Autoimage command not working Premila Samuel Mohan Dass
- Re: [AMBER] Autoimage command not working Daniel Roe
- Re: [AMBER] Autoimage command not working Martín Pettinati
- Re: [AMBER] Autoimage command not working Daniel Roe
- Re: [AMBER] RMSD of independent trajectories using cpptraj Hunter Wilson
- Re: [AMBER] Autoimage command not working Martín Pettinati
- [AMBER] Printing distance values to a file Sundar
- Re: [AMBER] Metal center molecule 高含露
Wednesday, 16 January 2019
- [AMBER] simulation with glycans Jacopo Sgrignani
- [AMBER] Separate work values for each restraint in SMD Sundar
- Re: [AMBER] simulation with glycans Sundar
- Re: [AMBER] Separate work values for each restraint in SMD Adrian Roitberg
- Re: [AMBER] Printing distance values to a file David A Case
- Re: [AMBER] Printing distance values to a file Sundar
- [AMBER] Can't put position restrains on ions Andrea H. Kasun
- Re: [AMBER] Separate work values for each restraint in SMD Sundar
- [AMBER] Introduction to dummy atoms needed Markowska
- Re: [AMBER] Introduction to dummy atoms needed Emmett Leddin
- Re: [AMBER] Can't put position restrains on ions David A Case
- [AMBER] Abrupt peaks in the RMSD plot of heating trajectory Amartya Pradhan
- Re: [AMBER] Abrupt peaks in the RMSD plot of heating trajectory Adrian Roitberg
- Re: [AMBER] Abrupt peaks in the RMSD plot of heating trajectory ABEL Stephane
- Re: [AMBER] Can't put position restrains on ions Pratul Agarwal
- Re: [AMBER] Can't put position restrains on ions Andrea H. Kasun
- Re: [AMBER] Can't put position restrains on ions Pratul Agarwal
- [AMBER] MCPB.py problem gaohanlu
Thursday, 17 January 2019
- [AMBER] Amber parameters for Boron atom Vincenzo Maria D'Amore
- [AMBER] pytraj Error: No reference set, cannot select by distance. Thomas Evangelidis
- [AMBER] time-dependent distance restraints Sundar
- [AMBER] Post to amber mailing list Debarati DasGupta
- [AMBER] LIE calculation in FEW workflow Debarati DasGupta
- [AMBER] How to convert a NetCDF format trajectory to separate PDB files in sequential order frame by frame Li, Dailin
- [AMBER] AMBER v18 on BG/Q Pratul Agarwal
- Re: [AMBER] How to convert a NetCDF format trajectory to separate PDB files in sequential order frame by frame Alechania Misturini
Friday, 18 January 2019
- [AMBER] [MGMS-DS]: Molecular Modelling Workshop + Tim Clark Birthday Symposium: April 08-11, 2019 in Erlangen, Germany Dr. Anselm Horn
- [AMBER] detecting bridging waters and ions with cpptraj Stefan Ivanov
- Re: [AMBER] time-dependent distance restraints David A Case
- Re: [AMBER] AMBER v18 on BG/Q David A Case
- [AMBER] Water bridge analysis using cpptraj (hbond) Abhilash J
- [AMBER] Xplor file generation Debarati DasGupta
- [AMBER] Entropy calculation with Interaction Entropy (IE) method Fulbabu Sk
- Re: [AMBER] pytraj Error: No reference set, cannot select by distance. Hai Nguyen
- Re: [AMBER] How to load and visualize large trajectories? Hai Nguyen
- [AMBER] pmemd18 mpi installation error Kateryna Miroshnychenko
- Re: [AMBER] How to load and visualize large trajectories? James Kress
Saturday, 19 January 2019
- Re: [AMBER] pmemd18 mpi installation error David Case
- Re: [AMBER] Amber parameters for Boron atom David Case
- Re: [AMBER] Metal center molecule Pengfei Li
- Re: [AMBER] MCPB.py problem Pengfei Li
- [AMBER] Fwd: Amber parameters for Boron atom Vincenzo Maria D'Amore
- Re: [AMBER] Zeolite simulations Pengfei Li
- Re: [AMBER] Fwd: Amber parameters for Boron atom David Case
- Re: [AMBER] Zeolite simulations Sundar
Sunday, 20 January 2019
- [AMBER] DNA-ligand system maya nair
- Re: [AMBER] DNA-ligand system Bill Ross
Monday, 21 January 2019
- [AMBER] regarding change in time Charu Sharma (JRF)
- Re: [AMBER] How to load and visualize large trajectories? Chetna Tyagi
- Re: [AMBER] Fwd: Amber parameters for Boron atom Vincenzo Maria D'Amore
- Re: [AMBER] MCPB.py problem 高含露
- [AMBER] MD with different velocities. Rinsha Chk
- Re: [AMBER] DNA-ligand system David A Case
- Re: [AMBER] regarding change in time David A Case
- Re: [AMBER] MD with different velocities. David A Case
- Re: [AMBER] pmemd18 mpi installation error Kateryna Miroshnychenko
- [AMBER] Suggestions on MM-(GB)PBSA Sundar
Tuesday, 22 January 2019
- [AMBER] Using Distance Restraints in TMD Aravind R
- [AMBER] PCA Analyze mode evec.pev Shirin Jamshidi
- [AMBER] recovering amber binaries Andreas Tosstorff
- Re: [AMBER] recovering amber binaries Gustaf Olsson
- Re: [AMBER] recovering amber binaries Pratul Agarwal
- [AMBER] lipidscd S.D. Stephan Schott
- Re: [AMBER] recovering amber binaries Andreas Tosstorff
- Re: [AMBER] lipidscd S.D. Daniel Roe
- Re: [AMBER] recovering amber binaries Daniel Roe
- [AMBER] MCPB.py Error Dylan Novack
- Re: [AMBER] How to load and visualize large trajectories? Hai Nguyen
- [AMBER] 2 types of Chlorine atom (one charge is -1 and other is -0.8) Saikat Pal
Wednesday, 23 January 2019
- Re: [AMBER] 2 types of Chlorine atom (one charge is -1 and other is -0.8) David A Case
- [AMBER] Creating a coarse-grained trajectory from an all atomistic simulation SARAH JEANNE LEFAVE
- [AMBER] pytraj native contacts Rosellen, Martin
- Re: [AMBER] pytraj native contacts Hai Nguyen
- Re: [AMBER] Creating a coarse-grained trajectory from an all atomistic simulation David A Case
- Re: [AMBER] pytraj native contacts Wesley Michael Botello-Smith
- Re: [AMBER] Creating a coarse-grained trajectory from an all atomistic simulation SARAH JEANNE LEFAVE
Thursday, 24 January 2019
- [AMBER] GPU cards RTX 2080Ti and Nvidia quadro 16GB RTX 5000 madhumalar arumugam
- [AMBER] Lifetime structural waters CPPTRAJ error Pedro Miguel Reis Figueiredo
- [AMBER] Combining CpHMD and aMD Cecilia Lindgren
- Re: [AMBER] Lifetime structural waters CPPTRAJ error Daniel Roe
- Re: [AMBER] Creating a coarse-grained trajectory from an all atomistic simulation Daniel Roe
- Re: [AMBER] pytraj native contacts Daniel Roe
- Re: [AMBER] Xplor file generation Daniel Roe
- Re: [AMBER] detecting bridging waters and ions with cpptraj Daniel Roe
- Re: [AMBER] PCA Analyze mode evec.pev Daniel Roe
- [AMBER] Simulation setup for LIE Debarati DasGupta
- Re: [AMBER] Simulation setup for LIE Bill Ross
- [AMBER] Unnatural nucleic acid in DNA chain Anthony Bogetti
- Re: [AMBER] Simulation setup for LIE Bill Ross
- Re: [AMBER] Unnatural nucleic acid in DNA chain Bill Ross
- [AMBER] Error in conversion from charmmgui to AMBER format Souvik Dey
- [AMBER] NMOD is not running for MM PBSA Santanu Santra
Friday, 25 January 2019
- [AMBER] Failed to compile mcres.F90 of Amber18+update.10 with ifort Motoshi Kamiya
- [AMBER] questions on VDW parameters Qinghua Liao
- [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Qinghua Liao
- Re: [AMBER] Unnatural nucleic acid in DNA chain David A Case
- Re: [AMBER] NMOD is not running for MM PBSA David A Case
- Re: [AMBER] Failed to compile mcres.F90 of Amber18+update.10 with ifort Charles Lin
- Re: [AMBER] Failed to compile mcres.F90 of Amber18+update.10 with ifort David A Case
- Re: [AMBER] questions on VDW parameters David A Case
- Re: [AMBER] Zeolite simulations David A Case
- Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water) Debarati DasGupta
- Re: [AMBER] MCPB.py error with HEME containing protein Pengfei Li
- Re: [AMBER] MCPB.py Error Pengfei Li
- Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water) Bill Ross
- Re: [AMBER] Introduction to dummy atoms needed Pengfei Li
- Re: [AMBER] Zeolite simulations Pengfei Li
- [AMBER] QM/MM dynamics: metal oxides emanuele falbo
- Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water) Bill Ross
- Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water) Debarati DasGupta
- [AMBER] Error Amber18 installation with Intel 19 compiler Bundit BOONYARIT
- Re: [AMBER] QM/MM dynamics: metal oxides emanuele falbo
- Re: [AMBER] Combining CpHMD and aMD Cruzeiro,Vinicius Wilian D
- Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water) Bill Ross
- [AMBER] Unusual separation between protein and ligand Rajarshi Roy
Saturday, 26 January 2019
- Re: [AMBER] Unusual separation between protein and ligand ABEL Stephane
- Re: [AMBER] QM/MM dynamics: metal oxides David Case
- Re: [AMBER] Unusual separation between protein and ligand Rajarshi Roy
- Re: [AMBER] Unusual separation between protein and ligand Stephan Schott
- Re: [AMBER] Error Amber18 installation with Intel 19 compiler David Case
- [AMBER] Interpreting MM-(GB)PBSA results Sundar
Sunday, 27 January 2019
- Re: [AMBER] MCPB.py error with HEME containing protein Prasanth G, Research Scholar
- Re: [AMBER] QM/MM dynamics: metal oxides emanuele
- [AMBER] Calculation of binding energy associated with a single water molecule Leena Aggarwal
- Re: [AMBER] Combining CpHMD and aMD Cecilia Lindgren
Monday, 28 January 2019
- Re: [AMBER] Combining CpHMD and aMD Cruzeiro,Vinicius Wilian D
- Re: [AMBER] Interpreting MM-(GB)PBSA results David A Case
- Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water) David A Case
- Re: [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. David A Case
- Re: [AMBER] Combining CpHMD and aMD Cecilia Lindgren
- Re: [AMBER] Combining CpHMD and aMD Cruzeiro,Vinicius Wilian D
- Re: [AMBER] Interpreting MM-(GB)PBSA results Josh Berryman
- Re: [AMBER] Calculation of binding energy associated with a single water molecule Pratul Agarwal
- Re: [AMBER] lipidscd S.D. Daniel Roe
- [AMBER] Amber force-filed parameters for amino-acid side chain analogues mish
- Re: [AMBER] lipidscd S.D. Stephan Schott
- Re: [AMBER] lipidscd S.D. Daniel Roe
- Re: [AMBER] Error in conversion from charmmgui to AMBER format Sally Pias
Tuesday, 29 January 2019
- [AMBER] Energy Calculation Mathematical Formula. DHEERAJ CHITARA
- Re: [AMBER] Energy Calculation Mathematical Formula. Daniel Roe
- Re: [AMBER] Amber force-filed parameters for amino-acid side chain analogues Pratul Agarwal
- Re: [AMBER] lipidscd S.D. Stephan Schott
- [AMBER] Set the correct number of CPUs and GPU - benchmark - Amber 14 Eduardo Almeida Costa
- Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water) David Case
Wednesday, 30 January 2019
- [AMBER] email MYRIAN TORRES RICO
- Re: [AMBER] MCPB.py Error Dylan Novack
- Re: [AMBER] Set the correct number of CPUs and GPU - benchmark - Amber 14 Ross Walker
- [AMBER] dihedral angles MYRIAN TORRES RICO
- Re: [AMBER] dihedral angles Hai Nguyen
- Re: [AMBER] dihedral angles diego.soler.uam.es
- Re: [AMBER] dihedral angles Charles-Alexandre Mattelaer
- [AMBER] Error while running MMPBSA.py Shagun Krishna
- Re: [AMBER] Interpreting MM-(GB)PBSA results Sundar
- Re: [AMBER] Interpreting MM-(GB)PBSA results Wesley Michael Botello-Smith
Thursday, 31 January 2019
- Re: [AMBER] Amber force-filed parameters for amino-acid side chain analogues mish
- Re: [AMBER] Amber force-filed parameters for amino-acid side chain analogues David A Case
- Re: [AMBER] Amber force-filed parameters for amino-acid side chain analogues mish
- Re: [AMBER] Amber force-filed parameters for amino-acid side chain analogues David Cerutti
- [AMBER] Problem regarding RMSD Saikat Pal
- Re: [AMBER] Problem regarding RMSD Saikat Pal
- [AMBER] pytraj time Shayna Hilburg
- Re: [AMBER] pytraj time Daniel Roe
- Re: [AMBER] pytraj time Shayna Hilburg

Last message date: Thu Jan 31 2019 - 13:00:02 PST
Archived on: Wed Nov 13 2024 - 05:55:44 PST

Amber Archive Jan 2019 by date