Amber Archive Dec 2017: by date

Thursday, 30 November 2017
- [AMBER] Error: No module named parmed.scripts Setyanto Md
- [AMBER] Problems with the "conbine" conmmand in LEaP 杨满意
- Re: [AMBER] imin=5 not working in AMBER16? Paul Mortenson
Friday, 1 December 2017
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! Gustavo Seabra
- [AMBER] implicit models for other solvents and non-standard solvents Vaibhav Dixit
- Re: [AMBER] Problems with the "conbine" conmmand in LEaP Daniel Roe
- Re: [AMBER] imin=5 not working in AMBER16? Daniel Roe
- Re: [AMBER] imin=5 not working in AMBER16? Paul Mortenson
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! Junmei Wang
- Re: [AMBER] imin=5 not working in AMBER16? David A Case
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! Sanaa ALAbbad
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! Sanaa ALAbbad
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! Junmei Wang
- Re: [AMBER] antechamber: prepgen mainchain file character limit Junmei Wang
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! mirzo
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! Sanaa ALAbbad
- Re: [AMBER] Problems with the "conbine" conmmand in LEaP 杨满意
Saturday, 2 December 2017
- [AMBER] Residue Protonation State Rana Rehan Khalid
- Re: [AMBER] Residue Protonation State Schmid, Ralf (Dr.)
- [AMBER] lipid 14 compatibility with FF14SB Chitrak Gupta
- [AMBER] Problem with running Example2 from MCPB.py reference SI file MinYuan
- [AMBER] MCPB.py to generate force field parameter for metal ion As3+ MinYuan
Sunday, 3 December 2017
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Lorenzo Gontrani
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ minyuan.mail.ustc.edu.cn
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Lorenzo Gontrani
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Lorenzo Gontrani
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ minyuan.mail.ustc.edu.cn
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Lorenzo Gontrani
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ MinYuan
- Re: [AMBER] lipid 14 compatibility with FF14SB David A Case
- [AMBER] Normalization of radial distribution function Szymon Żaczek
- Re: [AMBER] Error: No module named parmed.scripts Jason Swails
Monday, 4 December 2017
- Re: [AMBER] imin=5 not working in AMBER16? Paul Mortenson
- Re: [AMBER] Error: No module named parmed.scripts Setyanto Md
- [AMBER] helix broken during minimization step Rana Rehan Khalid
- Re: [AMBER] Normalization of radial distribution function George M. Giambasu
- [AMBER] GPU workstation with 8 x nVidia GTX 1080 Ti Hadházi Ádám
- Re: [AMBER] GPU workstation with 8 x nVidia GTX 1080 Ti Ross Walker
- Re: [AMBER] GPU workstation with 8 x nVidia GTX 1080 Ti Carlos Simmerling
- Re: [AMBER] GPU workstation with 8 x nVidia GTX 1080 Ti Ross Walker
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Pengfei Li
- Re: [AMBER] Problem with running Example2 from MCPB.py reference SI file Pengfei Li
- Re: [AMBER] MCPB.py how to insert the heteroatom heme in the one domain of macromolecule Pengfei Li
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ MinYuan
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ MinYuan
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Lorenzo Gontrani
Tuesday, 5 December 2017
- Re: [AMBER] Normalization of radial distribution function Szymon Żaczek
- [AMBER] To calculate TI using soft-core potential or not Yang Jinpeng
- Re: [AMBER] Normalization of radial distribution function Batuhan Kav
- Re: [AMBER] Normalization of radial distribution function Szymon Żaczek
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ MinYuan
- Re: [AMBER] Problem with running Example2 from MCPB.py reference SI file MinYuan
- Re: [AMBER] To calculate TI using soft-core potential or not Daniel Mermelstein
- [AMBER] how to generate paramaters for GlcNH3 Tarsis
- Re: [AMBER] how to generate paramaters for GlcNH3 Bill Ross
- [AMBER] generation of topology and coordinate for glycan Rajarshi Roy
- Re: [AMBER] generation of topology and coordinate for glycan Bill Ross
- Re: [AMBER] generation of topology and coordinate for glycan Rajarshi Roy
- Re: [AMBER] generation of topology and coordinate for glycan Bill Ross
- [AMBER] Problem in visualizing Amber16 trajecories in VMD Biplab Ghosh
- Re: [AMBER] Problem in visualizing Amber16 trajecories in VMD Bill Ross
- Re: [AMBER] Problem in visualizing Amber16 trajecories in VMD Abdul-Rashid III Sampaco
Wednesday, 6 December 2017
- Re: [AMBER] Problem in visualizing Amber16 trajecories in VMD David A Case
- [AMBER] Amber Protonate for H++ Andreas Tosstorff
- Re: [AMBER] Amber Protonate for H++ David A Case
- Re: [AMBER] Amber Protonate for H++ Setyanto Md
- [AMBER] The paramters of frcmod.chcl3 Yang Jinpeng
Thursday, 7 December 2017
- Re: [AMBER] Amber Protonate for H++ Andreas Tosstorff
- Re: [AMBER] Amber Protonate for H++ Andreas Tosstorff
- [AMBER] force addions to avoid replacing specific solvent molecules by ions Vlad Cojocaru
- Re: [AMBER] force addions to avoid replacing specific solvent molecules by ions Bill Ross
- Re: [AMBER] force addions to avoid replacing specific solvent molecules by ions Vlad Cojocaru
- Re: [AMBER] force addions to avoid replacing specific solvent molecules by ions Bill Ross
- Re: [AMBER] force addions to avoid replacing specific solvent molecules by ions Vlad Cojocaru
- [AMBER] Modified amino acid Rajarshi Roy
- Re: [AMBER] Modified amino acid junmwang.gmail.com
- Re: [AMBER] Modified amino acid Rajarshi Roy
- Re: [AMBER] Amber Protonate for H++ Setyanto Md
- Re: [AMBER] Modified amino acid Junmei Wang
- [AMBER] pdf of O-GlcNAc Ser and Thr Yin, Guowei
- [AMBER] pdf of O-GlcNAc Ser and Thr Yin, Guowei
- [AMBER] End-of-File error occurring for Minimization run using Amoeba Force Field Chase Zagorec-Marks
- [AMBER] pdf of O-GlcNAc Ser and Thr Li, Xinghui
- Re: [AMBER] how to generate paramaters for GlcNH3 Tarsis
- Re: [AMBER] generation of topology and coordinate for glycan Lachele Foley
- Re: [AMBER] pdf of O-GlcNAc Ser and Thr Lachele Foley
- [AMBER] Bonds between residues are broken Shilpa Gupta
Friday, 8 December 2017
- [AMBER] Does pmemd.cuda support QM/MM MinYuan
- Re: [AMBER] Modified amino acid Rajarshi Roy
- Re: [AMBER] Does pmemd.cuda support QM/MM Elvis Martis
- Re: [AMBER] Amber Protonate for H++ David A Case
- Re: [AMBER] End-of-File error occurring for Minimization run using Amoeba Force Field David A Case
- Re: [AMBER] Bonds between residues are broken David A Case
- Re: [AMBER] Bonds between residues are broken Shilpa Gupta
- Re: [AMBER] how to generate paramaters for GlcNH3 Tarsis Ferreira
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Dow Hurst
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER David Cerutti
- [AMBER] Problem of loading complex Mustafa Alhaji Isa
- Re: [AMBER] Problem of loading complex Carlos Simmerling
- Re: [AMBER] Problem of loading complex Mustafa Alhaji Isa
- Re: [AMBER] how to generate paramaters for GlcNH3 Lachele Foley
- Re: [AMBER] Problem of loading complex Carlos Simmerling
- Re: [AMBER] Problem of loading complex David A Case
Saturday, 9 December 2017
- Re: [AMBER] Does pmemd.cuda support QM/MM MinYuan
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Ross Walker
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Scott Le Grand
Sunday, 10 December 2017
- [AMBER] Solvating a molecule in amber Shilpa Gupta
- Re: [AMBER] Solvating a molecule in amber Bill Ross
- Re: [AMBER] Solvating a molecule in amber Shilpa Gupta
- Re: [AMBER] Solvating a molecule in amber Bill Ross
Monday, 11 December 2017
- [AMBER] Queries about aMD simulation of metal-bound membrane protein and anu chandra
- [AMBER] MCPB HEME Rana Rehan Khalid
- Re: [AMBER] MCPB HEME Bill Ross
- Re: [AMBER] Solvating a molecule in amber Shilpa Gupta
- Re: [AMBER] Solvating a molecule in amber Bill Ross
- Re: [AMBER] Solvating a molecule in amber Shilpa Gupta
- Re: [AMBER] MCPB HEME Marcos Serrou do Amaral
- Re: [AMBER] MCPB HEME Rana Rehan Khalid
- [AMBER] cpptraj segmentation fault Andreas Tosstorff
- Re: [AMBER] cpptraj segmentation fault Daniel Roe
- Re: [AMBER] cpptraj segmentation fault Andreas Tosstorff
- Re: [AMBER] cpptraj segmentation fault Daniel Roe
- Re: [AMBER] cpptraj segmentation fault Andreas Tosstorff
- Re: [AMBER] cpptraj segmentation fault Daniel Roe
- Re: [AMBER] cpptraj segmentation fault Daniel Roe
Tuesday, 12 December 2017
- [AMBER] MCPB.py deal with two metal-like sites simultaneously MinYuan
- Re: [AMBER] Does pmemd.cuda support QM/MM Rivera, Miguel
- [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Myron
- Re: [AMBER] Does pmemd.cuda support QM/MM David Cerutti
- Re: [AMBER] Does pmemd.cuda support QM/MM Elvis Martis
- Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Carlos Simmerling
- Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Daniel Roe
- [AMBER] error when running tleap from script, works fine from shell Andreas Tosstorff
- [AMBER] MMPBSA.py and S-S bonds between different chains Sergey Samsonov
- Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Myron
- Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Myron
- [AMBER] Error with installation, amber 17 on centos server Praneeth Bommisetti
- Re: [AMBER] Error with installation, amber 17 on centos server Hai Nguyen
- Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Carlos Simmerling
- [AMBER] Fwd: Re: Error with installation, amber 17 on centos server Praneeth Bommisetti
- Re: [AMBER] Error with installation, amber 17 on centos server Tru Huynh
- [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib MinYuan
Wednesday, 13 December 2017
- [AMBER] Parmed topology file have ifbox=0 Shilpa Gupta
- Re: [AMBER] error when running tleap from script, works fine from shell David A Case
- [AMBER] MM-GBSA, acquire the value of each frame Giovanni Grazioso
- Re: [AMBER] MM-GBSA, acquire the value of each frame Casalini Tommaso
- Re: [AMBER] MM-GBSA, acquire the value of each frame Dolivier
- Re: [AMBER] MCPB.py deal with two metal-like sites simultaneously Pengfei Li
- Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib Pengfei Li
- [AMBER] T.I. Sidechain setup (softcore potential) based off of A9 tutorial Andrew Schaub
- [AMBER] PCA.CPPTRAJ Rana Rehan Khalid
- Re: [AMBER] autoimage for a protein filament Baker, Joseph
Thursday, 14 December 2017
- [AMBER] query regarding restraint_wt Leena Aggarwal
- Re: [AMBER] query regarding restraint_wt Bill Ross
- Re: [AMBER] query regarding restraint_wt Leena Aggarwal
- Re: [AMBER] query regarding restraint_wt Bill Ross
- Re: [AMBER] query regarding restraint_wt Carlos Simmerling
- Re: [AMBER] autoimage for a protein filament Daniel Roe
- [AMBER] TI softcore single topology (HIE to HIP) - How do I generate a new lib file for an existing residue? Andrew Schaub
- Re: [AMBER] TI softcore single topology (HIE to HIP) - How do I generate a new lib file for an existing residue? Andrew Schaub
- Re: [AMBER] PCA.CPPTRAJ Daniel Roe
- Re: [AMBER] TI softcore single topology (HIE to HIP) - How do I generate a new lib file for an existing residue? Andrew Schaub
- Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid
- [AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords Investigador Química
- [AMBER] HREMD run Dr. MANAS MONDAL
Friday, 15 December 2017
- Re: [AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords David A Case
- Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib MinYuan
- Re: [AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords Elvis Martis
- Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib Bill Ross
- Re: [AMBER] HREMD run Daniel Roe
- Re: [AMBER] PCA.CPPTRAJ Daniel Roe
- Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib Pengfei Li
Saturday, 16 December 2017
- Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid
- [AMBER] Leap not running Naina Singh
- Re: [AMBER] Leap not running Bill Ross
- Re: [AMBER] Leap not running David A Case
- Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid
- Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid
- Re: [AMBER] autoimage for a protein filament Baker, Joseph
Sunday, 17 December 2017
- [AMBER] CPPTRAJ hbond Analysis Rana Rehan Khalid
- Re: [AMBER] T.I. Sidechain setup (softcore potential) based off of A9 tutorial Daniel Mermelstein
- Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib minyuan.mail.ustc.edu.cn
Monday, 18 December 2017
- [AMBER] cpptraj multiple trajectories Andreas Tosstorff
- Re: [AMBER] CPPTRAJ hbond Analysis Hai Nguyen
- Re: [AMBER] CPPTRAJ hbond Analysis Rana Rehan Khalid
- Re: [AMBER] HREMD run Dr. MANAS MONDAL
- [AMBER] Several questions about Amber adaptive QM/MM MD. Mingyuan_xu
- Re: [AMBER] cpptraj multiple trajectories Daniel Roe
- Re: [AMBER] HREMD run Daniel Roe
- Re: [AMBER] CPPTRAJ hbond Analysis Daniel Roe
- Re: [AMBER] PCA.CPPTRAJ Daniel Roe
- Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid
- Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid
- Re: [AMBER] CPPTRAJ hbond Analysis Rana Rehan Khalid
- Re: [AMBER] HREMD run Dr. MANAS MONDAL
- [AMBER] Water-slab at constant pressure jesus berlanga
- Re: [AMBER] HREMD run Hai Nguyen
- [AMBER] box coordinates of the trajectory Leena Aggarwal
- Re: [AMBER] box coordinates of the trajectory Bill Ross
Tuesday, 19 December 2017
- [AMBER] [MGMS-DS]: Molecular Modelling Workshop March 12-14, 2018 in Erlangen, Germany Dr. Anselm Horn
- Re: [AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords Investigador Química
- Re: [AMBER] Water-slab at constant pressure David A Case
- Re: [AMBER] box coordinates of the trajectory Daniel Roe
- Re: [AMBER] CPPTRAJ hbond Analysis Daniel Roe
- Re: [AMBER] PCA.CPPTRAJ Daniel Roe
- Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid
Wednesday, 20 December 2017
- Re: [AMBER] CPPTRAJ hbond Analysis Rana Rehan Khalid
- [AMBER] more than 100% hydrogen bond population Thakur, Abhishek
- [AMBER] error in distance restraints Michael Shokhen
- Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib Pengfei Li
- Re: [AMBER] error in distance restraints David A Case
Thursday, 21 December 2017
- [AMBER] Function name not recognized in RdPar Rinsha Chk
- Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid
- Re: [AMBER] Function name not recognized in RdPar David A Case
- Re: [AMBER] Function name not recognized in RdPar Rinsha Chk
- Re: [AMBER] Function name not recognized in RdPar Rinsha Chk
- [AMBER] parmed error Thakur, Abhishek
- Re: [AMBER] parmed error p.kartheek
- [AMBER] Binding energy of ligand with homology model Morrow,John Kenneth
- Re: [AMBER] parmed error Hai Nguyen
Friday, 22 December 2017
- [AMBER] Atom restraints in AMBER Nikolay N. Kuzmich
- [AMBER] Meltcurve cpptraj Andreas Tosstorff
- Re: [AMBER] Meltcurve cpptraj Daniel Roe
- Re: [AMBER] Several questions about Amber adaptive QM/MM MD. Goetz, Andreas
Saturday, 23 December 2017
- [AMBER] hbond occupancy plot cpptraj Rana Rehan Khalid
Sunday, 24 December 2017
- Re: [AMBER] hbond occupancy plot cpptraj Rana Rehan Khalid
Tuesday, 26 December 2017
- [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish
- [AMBER] Fwd: A small but fatal Typo in "LEaP Tutorial" Gao Zhenting
- [AMBER] Unable to compile mixed C/Fortran code. suma jayakrishnan
- Re: [AMBER] Unable to compile mixed C/Fortran code. Bill Ross
- Re: [AMBER] Unable to compile mixed C/Fortran code. David A Case
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? David Cerutti
- [AMBER] Troubling changes to NVIDIA Driver EULA Ross Walker
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA Charles-Alexandre Mattelaer
- Re: [AMBER] A small but fatal Typo in "LEaP Tutorial" Pengfei Li
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA David Cerutti
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA Ross Walker
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA David Cerutti
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA Ross Walker
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA Bill Ross
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA Bill Ross
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Bill Ross
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA Robert Molt
- Re: [AMBER] A small but fatal Typo in "LEaP Tutorial" Gao Zhenting
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Bill Ross
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish
Wednesday, 27 December 2017
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Bill Ross
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish
- [AMBER] Which potential is used in TIP3P (How to calculate EPot by hand) Johannes Kalliauer
- Re: [AMBER] Which potential is used in TIP3P (How to calculate EPot by hand) David Cerutti
- Re: [AMBER] Which potential is used in TIP3P (How to calculate EPot by hand) David A Case
- [AMBER] NTWR,NTWX, NTPR increases for rest of simulation. Rana Rehan Khalid
- Re: [AMBER] NTWR,NTWX, NTPR increases for rest of simulation. David A Case
- Re: [AMBER] NTWR,NTWX, NTPR increases for rest of simulation. Rana Rehan Khalid
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley
Thursday, 28 December 2017
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish
- [AMBER] Phosphohistidine residues Jan Ludwiczak
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley
Friday, 29 December 2017
- [AMBER] CPPTRAJ HBOND Rana Rehan Khalid
- Re: [AMBER] CPPTRAJ HBOND Daniel Roe
- Re: [AMBER] CPPTRAJ HBOND Charles-Alexandre Mattelaer
- Re: [AMBER] CPPTRAJ HBOND Rana Rehan Khalid
Sunday, 31 December 2017
- [AMBER] DSSP CPPtraj Rana Rehan Khalid
- Re: [AMBER] DSSP CPPtraj Rana Rehan Khalid

Last message date: Sun Dec 31 2017 - 07:30:02 PST
Archived on: Fri Apr 19 2024 - 05:55:23 PDT

Amber Archive Dec 2017 by date