Amber Archive May 2017: by date

Sunday, 30 April 2017
- Re: [AMBER] External electric fields on CUDA enabled PMEMD Charles Lin
- [AMBER] Missing File: charmmlipid2amber.csv Alexander Adams
Monday, 1 May 2017
- Re: [AMBER] Missing File: charmmlipid2amber.csv Elvis Martis
- Re: [AMBER] Restraint in Steered MD/Jarzynski method Hannes Loeffler
- Re: [AMBER] [SPAM] Re: consult about LEaP in amber 张壮壮
- Re: [AMBER] does not have a type Sowmya Indrakumar
- Re: [AMBER] does not have a type Thakur, Abhishek
- Re: [AMBER] does not have a type David Case
- Re: [AMBER] Too many iterations in routine! in RMSD calculation Daniel Roe
- Re: [AMBER] Too many iterations in routine! in RMSD calculation kungking Hanpaibool
- Re: [AMBER] Too many iterations in routine! in RMSD calculation Daniel Roe
- Re: [AMBER] Too many iterations in routine! in RMSD calculation kungking Hanpaibool
- Re: [AMBER] Too many iterations in routine! in RMSD calculation kungking Hanpaibool
- Re: [AMBER] Restraint in Steered MD/Jarzynski method Ramin Salimi
- Re: [AMBER] Too many iterations in routine! in RMSD calculation Daniel Roe
- [AMBER] Find entropy from non-equilibrium free energy calculation Ramin Salimi
- [AMBER] acdoctor: fatal error when reading carboxylates from .mol2 files Niel Henriksen
- [AMBER] glycoprotein Neha Gandhi
Tuesday, 2 May 2017
- Re: [AMBER] glycoprotein Neha Gandhi
- Re: [AMBER] Find entropy from non-equilibrium free energy calculation Hannes Loeffler
- Re: [AMBER] acdoctor: fatal error when reading carboxylates from .mol2 files Scott Brozell
- Re: [AMBER] Find entropy from non-equilibrium free energy calculation Ramin Salimi
- [AMBER] MD under external electric field & GPUs parallel problem 吴萌
- [AMBER] Fwd: failed to generate parameter and topology file for protein-ligand complex containing zinc Sharon D. Morris
- [AMBER] AddtoBox failure sylvester kisembo
- Re: [AMBER] Fwd: failed to generate parameter and topology file for protein-ligand complex containing zinc Elvis Martis
- Re: [AMBER] Error with 'surf' and acetonitrile-water solvent mixture Daniel Roe
- [AMBER] Regarding amber-gaussian QM/MM problem Budhathoki, Dipesh
- Re: [AMBER] Regarding amber-gaussian QM/MM problem Goetz, Andreas
- [AMBER] Ambertools coulomb constant Gard Nelson
- Re: [AMBER] AddtoBox failure David Case
- Re: [AMBER] AddtoBox failure David Cerutti
Wednesday, 3 May 2017
- [AMBER] ntx=5 and ntx=7 (Sanderinput) Johannes Kalliauer
- [AMBER] Question on implementing igb=8, along with mbondi3 Ramin Salimi
- Re: [AMBER] ntx=5 and ntx=7 (Sanderinput) Hannes Loeffler
- Re: [AMBER] Question on implementing igb=8, along with mbondi3 Carlos Simmerling
- Re: [AMBER] DNA Tutorial B1 - Temperature Drop Johannes Kalliauer
- Re: [AMBER] ntx=5 and ntx=7 (Sanderinput) David Case
- Re: [AMBER] DNA Tutorial B1 - Temperature Drop David Case
- Re: [AMBER] AddToBox Failure David Case
- Re: [AMBER] Ambertools coulomb constant David Case
- [AMBER] LEaP failing after update to AmberTools17 Charles-Alexandre Mattelaer
- Re: [AMBER] LEaP failing after update to AmberTools17 David Case
- Re: [AMBER] LEaP failing after update to AmberTools17 Charles-Alexandre Mattelaer
- [AMBER] Question about the pairwise option in cpptraj David Case
- [AMBER] The problem for image tool in AMBER 鲁俊波
- [AMBER] How to restart MD Garima Singh
Thursday, 4 May 2017
- Re: [AMBER] How to restart MD Andreas Tosstorff
- Re: [AMBER] How to restart MD Elvis Martis
- [AMBER] GPUs parallel problem Meng Wu
- [AMBER] aMD and cpH-MD Hofer, Florian
- Re: [AMBER] GPUs parallel problem Andreas Tosstorff
- Re: [AMBER] GPUs parallel problem Gulsevin,Alican
- Re: [AMBER] Error with 'surf' and acetonitrile-water solvent mixture Daniel Roe
- Re: [AMBER] GPUs parallel problem Ross Walker
- Re: [AMBER] The problem for image tool in AMBER Daniel Roe
- Re: [AMBER] Error with 'surf' and acetonitrile-water solvent mixture Daniel Roe
- Re: [AMBER] The problem for image tool in AMBER 鲁俊波
- Re: [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber. Miguel Rivera
Friday, 5 May 2017
- [AMBER] ff parameters Andrea Spitaleri
- Re: [AMBER] intra-residue water bridge with cpptraj Joanna Sarzynska
- Re: [AMBER] GPUs parallel problem Meng Wu
- Re: [AMBER] ff parameters David Case
- Re: [AMBER] GPUs parallel problem Ross Walker
- Re: [AMBER] intra-residue water bridge with cpptraj Daniel Roe
- Re: [AMBER] The problem for image tool in AMBER Daniel Roe
- Re: [AMBER] Error with 'surf' and acetonitrile-water solvent mixture Marcel Passon
- Re: [AMBER] Regarding amber-gaussian QM/MM problem Budhathoki, Dipesh
- Re: [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber. Daniel Roe
- Re: [AMBER] ff parameters Jason Swails
- [AMBER] Fast 3-point water residue error for coordinates generated with parmed Sadegh Faramarzi Ganjabad
- Re: [AMBER] Question about the pairwise option in cpptraj Daniel Roe
- Re: [AMBER] Fast 3-point water residue error for coordinates generated with parmed Daniel Roe
- Re: [AMBER] ff parameters Andrea Spitaleri
- Re: [AMBER] ff parameters Hai Nguyen
Saturday, 6 May 2017
- Re: [AMBER] ff parameters David Case
Sunday, 7 May 2017
- [AMBER] Cellulose simulation luca maggi
- [AMBER] Molecule with glyco - single amino acid linkage? yunshi11 .
- Re: [AMBER] Molecule with glyco - single amino acid linkage? Lachele Foley
- [AMBER] Atom type assignment by Antechamber Matsuura, Azuma
- Re: [AMBER] Fast 3-point water residue error for coordinates Sadegh Faramarzi Ganjabad
Monday, 8 May 2017
- Re: [AMBER] Cellulose simulation Lachele Foley
- Re: [AMBER] Cellulose simulation luca maggi
- Re: [AMBER] ff parameters Jason Swails
- [AMBER] Parameterization Ligand Boron Pedro Fernandes
- Re: [AMBER] Parameterization Ligand Boron Elvis Martis
- [AMBER] Cpptraj calculates only three PHI-PSI angles in a 18-residue long peptide Chetna Tyagi
- Re: [AMBER] Cpptraj calculates only three PHI-PSI angles in a 18-residue long peptide Daniel Roe
- Re: [AMBER] Atom type assignment by Antechamber Junmei Wang
- Re: [AMBER] Fast 3-point water residue error for coordinates Song-Ho Chong
- Re: [AMBER] Cpptraj calculates only three PHI-PSI angles in a 18-residue long peptide Elvis Martis
- [AMBER] tleap-incorpoarating .frcmod, .prep files for unnatural nucleotides p.kartheek
- Re: [AMBER] Cpptraj calculates only three PHI-PSI angles in a 18-residue long peptide Chetna Tyagi
- Re: [AMBER] Cpptraj calculates only three PHI-PSI angles in a 18-residue long peptide Daniel Roe
- Re: [AMBER] Fast 3-point water residue error for coordinates Sadegh Faramarzi Ganjabad
- Re: [AMBER] Molecule with glyco - single amino acid linkage? yunshi11 .
- [AMBER] Possible bug in the GPU code Pratul K. Agarwal
- Re: [AMBER] Atom type assignment by Antechamber Matsuura, Azuma
- Re: [AMBER] Possible bug in the GPU code David Case
- Re: [AMBER] tleap-incorpoarating .frcmod, .prep files for unnatural nucleotides Elvis Martis
Tuesday, 9 May 2017
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Paul Westphaelinger
- [AMBER] Amber parameters for CPD and 6-4PP p.kartheek
- Re: [AMBER] Amber parameters for CPD and 6-4PP Elvis Martis
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Charles Lin
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Pratul K. Agarwal
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Charles Lin
- [AMBER] Problem in splitting mdcrd file with cpptraj Manjula Saravanan
Wednesday, 10 May 2017
- [AMBER] Two questions for GAFF Matsuura, Azuma
- [AMBER] Distance regarding to interface between two solvents Habib Rozale
- [AMBER] fcc_metals.lib is not a valid databae Sohag Biswas
- [AMBER] how to draw Radial Distribution Functions? Yang Jinpeng
- [AMBER] MG angle parameter Tommaso Biagini
- Re: [AMBER] Two questions for GAFF Junmei Wang
- [AMBER] question about commutation of sub-trajectories and frame aligning Gordon Richard Chalmers
- Re: [AMBER] MG angle parameter Elvis Martis
- Re: [AMBER] MG angle parameter Tommaso Biagini
- Re: [AMBER] MG angle parameter kungking Hanpaibool
- Re: [AMBER] question about commutation of sub-trajectories and frame aligning Daniel Roe
- Re: [AMBER] Problem in splitting mdcrd file with cpptraj Daniel Roe
- Re: [AMBER] how to draw Radial Distribution Functions? Daniel Roe
- Re: [AMBER] question about commutation of sub-trajectories and frame aligning Gordon Richard Chalmers
- [AMBER] CX1 missing connect0 atom._MCPB Thakur, Abhishek
- Re: [AMBER] CX1 missing connect0 atom._MCPB Pengfei Li
- Re: [AMBER] Two questions for GAFF Matsuura, Azuma
- Re: [AMBER] External electric fields on CUDA enabled PMEMD Neville Bethel
- Re: [AMBER] MG angle parameter Tommaso Biagini
- Re: [AMBER] External electric fields on CUDA enabled PMEMD Charles Lin
- Re: [AMBER] MG angle parameter Elvis Martis
- Re: [AMBER] MG angle parameter Tommaso Biagini
Thursday, 11 May 2017
- [AMBER] ERROR: Could not read coords from .rst file Vishal Nemaysh
- Re: [AMBER] ERROR: Could not read coords from .rst file Szymon Żaczek
- [AMBER] Water Analysis with SPAM julian.zachmann selvita.home.pl
- [AMBER] Tip3p water box size for two different systems. Saman Yousuf ali
- [AMBER] <Na 1> Could not find vdW (or other) parameters for type: Na Thakur, Abhishek
- Re: [AMBER] <Na 1> Could not find vdW (or other) parameters for type: Na David A Case
- Re: [AMBER] <Na 1> Could not find vdW (or other) parameters for type: Na Thakur, Abhishek
- Re: [AMBER] Tip3p water box size for two different systems. Elvis Martis
- [AMBER] Fwd: Problem in splitting mdcrd file with cpptraj Manjula Saravanan
- Re: [AMBER] Tip3p water box size for two different systems. Saman Yousuf ali
- Re: [AMBER] Tip3p water box size for two different systems. Elvis Martis
- Re: [AMBER] Tip3p water box size for two different systems. Bill Ross
Friday, 12 May 2017
- [AMBER] How to use Amber in HPC Garima Singh
- Re: [AMBER] How to use Amber in HPC Elvis Martis
- Re: [AMBER] <Na 1> Could not find vdW (or other) parameters for type: Na David A Case
- [AMBER] EEL and VDW Notification on minimization with sander/pmemd Charles Mariasoosai
- [AMBER] Has Hessian printing been added? Eric Hansen
Saturday, 13 May 2017
- Re: [AMBER] EEL and VDW Notification on minimization with sander/pmemd Elvis Martis
- [AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin') Ramin Salimi
- Re: [AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin') Elvis Martis
- Re: [AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin') Elvis Martis
- Re: [AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin') Ramin Salimi
- Re: [AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin') Elvis Martis
- [AMBER] MCPB and Can not run MD simulation; some residue move out of protein kungking Hanpaibool
- Re: [AMBER] MCPB and Can not run MD simulation; some residue move out of protein Elvis Martis
- Re: [AMBER] MCPB and Can not run MD simulation; some residue move out of protein kungking Hanpaibool
- Re: [AMBER] MCPB and Can not run MD simulation; some residue move out of protein Bill Ross
Sunday, 14 May 2017
- Re: [AMBER] EEL and VDW Notification on minimization with sander/pmemd David Case
- Re: [AMBER] Has Hessian printing been added? David Case
- Re: [AMBER] MCPB and Can not run MD simulation; some residue move out of protein David Case
- [AMBER] dimer rmsd issue. Saman Yousuf ali
- Re: [AMBER] dimer rmsd issue. Elvis Martis
- Re: [AMBER] dimer rmsd issue. Bill Ross
Monday, 15 May 2017
- [AMBER] Fwd: Request for troubleshoot in MAWS (igem software from Heidelberg) based on AMBER Abudhahir Buhari
- Re: [AMBER] Water Analysis with SPAM julian.zachmann selvita.home.pl
- Re: [AMBER] Water Analysis with SPAM Bill Ross
- Re: [AMBER] Water Analysis with SPAM julian.zachmann selvita.home.pl
- Re: [AMBER] Water Analysis with SPAM Bill Ross
- Re: [AMBER] Water Analysis with SPAM Bill Ross
- Re: [AMBER] Water Analysis with SPAM Bill Ross
- Re: [AMBER] Water Analysis with SPAM julian.zachmann selvita.home.pl
- Re: [AMBER] Water Analysis with SPAM Bill Ross
- Re: [AMBER] Water Analysis with SPAM julian.zachmann selvita.home.pl
- [AMBER] Partial Mini error Nikita Devnarain
- Re: [AMBER] <Na 1> Could not find vdW (or other) parameters for type: Na Thakur, Abhishek
- [AMBER] Ante_R.E.D script files. Vatsal Purohit
- Re: [AMBER] Water Analysis with SPAM Bill Ross
- Re: [AMBER] <Na 1> Could not find vdW (or other) parameters for type: Na Bill Ross
- Re: [AMBER] Partial Mini error David Case
- [AMBER] Reference structure for targeted MD Francesco Gentile
Tuesday, 16 May 2017
- [AMBER] convergence question about xmin liu junjun
- Re: [AMBER] Reference structure for targeted MD David Case
- [AMBER] sander API data structure Brent Krueger
- Re: [AMBER] Water Analysis with SPAM Daniel Roe
- Re: [AMBER] sander API data structure Daniel Roe
- Re: [AMBER] Water Analysis with SPAM julian.zachmann selvita.home.pl
- Re: [AMBER] dimer rmsd issue. Daniel Roe
- Re: [AMBER] Water Analysis with SPAM Daniel Roe
- Re: [AMBER] sander API data structure Hai Nguyen
- Re: [AMBER] Water Analysis with SPAM julian.zachmann selvita.home.pl
- Re: [AMBER] Reference structure for targeted MD Daniel Roe
- Re: [AMBER] Water Analysis with SPAM Daniel Roe
- Re: [AMBER] sander API data structure Brent Krueger
- Re: [AMBER] sander API data structure Jason Swails
- Re: [AMBER] sander API data structure Bill Ross
- [AMBER] Building distributable executable D'Auria, Raffaella
Wednesday, 17 May 2017
- [AMBER] addions doubt Mary Varughese
- [AMBER] resp charges Jacopo Sgrignani
- Re: [AMBER] addions doubt Bill Ross
- [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Ramin Salimi
- Re: [AMBER] resp charges Alessandro Contini
- Re: [AMBER] resp charges Artem Shekhovtsov
- Re: [AMBER] resp charges Andrea Spitaleri
- Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Hannes Loeffler
- Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Ramin Salimi
- Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Hannes Loeffler
- Re: [AMBER] resp charges David Cerutti
- [AMBER] Problem with parmed Qinghua Liao
- Re: [AMBER] Problem with parmed Hannes Loeffler
- Re: [AMBER] Problem with parmed Qinghua Liao
- Re: [AMBER] Problem with parmed Jason Swails
- Re: [AMBER] Problem with parmed Qinghua Liao
- Re: [AMBER] Building distributable executable David Case
- Re: [AMBER] resp charges Jones de Andrade
- [AMBER] early bird deadline extended Thomas Exner
- Re: [AMBER] Building distributable executable Scott Brozell
- Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Ramin Salimi
- Re: [AMBER] convergence question about xmin liu junjun
- Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Adrian Roitberg
- Re: [AMBER] Building distributable executable Jason Swails
- Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Ramin Salimi
- [AMBER] Doubt about EVB/LES-PIMD Stregone
- Re: [AMBER] Building distributable executable Scott Brozell
- Re: [AMBER] convergence question about xmin Scott Brozell
- [AMBER] understanding results Carlos Romero
- Re: [AMBER] Building distributable executable Daniel Roe
- [AMBER] Implicit solvation method giving the error number of triangulated 3-point waters found: 0 Ramin Salimi
- Re: [AMBER] Implicit solvation method giving the error number of triangulated 3-point waters found: 0 Adrian Roitberg
- Re: [AMBER] Implicit solvation method giving the error number of triangulated 3-point waters found: 0 Ramin Salimi
- [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Ramin Salimi
- Re: [AMBER] Building distributable executable D'Auria, Raffaella
- Re: [AMBER] Implicit solvation method giving the error number of triangulated 3-point waters found: 0 David Case
- Re: [AMBER] Implicit solvation method giving the error number of triangulated 3-point waters found: 0 David Case
- Re: [AMBER] Building distributable executable Scott Brozell
- [AMBER] [Amber16]"cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" 冯国强
- [AMBER] [Amber16]"cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" 冯国强
Thursday, 18 May 2017
- Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Hannes Loeffler
- [AMBER] reference or custom GPUs? Hadházi Ádám
- [AMBER] Could not find vdW (or other) parameters for type: Na+ Michael Shokhen
- Re: [AMBER] resp charges FyD
- Re: [AMBER] Could not find vdW (or other) parameters for type: Na+ Elvis Martis
- Re: [AMBER] [Amber16]"cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" Elvis Martis
- Re: [AMBER] Doubt about EVB/LES-PIMD David A Case
- Re: [AMBER] understanding results David A Case
- Re: [AMBER] [Amber16]"cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" David A Case
- Re: [AMBER] Could not find vdW (or other) parameters for type: Na+ David A Case
- [AMBER] phosaa10 reference Jacopo Sgrignani
- Re: [AMBER] phosaa10 reference David A Case
- [AMBER] possible bug for reading &qmmm after &lmod liu junjun
- Re: [AMBER] MCPB and Can not run MD simulation; some residue move out of protein Pengfei Li
- Re: [AMBER] possible bug for reading &qmmm after &lmod Scott Brozell
- Re: [AMBER] [Amber16]"cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" Scott Brozell
- [AMBER] cpptraj nastruct local helical vectors? Kenneth Huang
- Re: [AMBER] Building distributable executable Scott Brozell
- [AMBER] Help with PB simulations using MPI Jake
- [AMBER] Amber Error Jerrano Bowleg
- Re: [AMBER] Amber Error Bill Ross
- Re: [AMBER] Help with PB simulations using MPI Ray Luo
- Re: [AMBER] [Amber16]"cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" Ross Walker
- Re: [AMBER] reference or custom GPUs? Ross Walker
- Re: [AMBER] reference or custom GPUs? Scott Le Grand
- Re: [AMBER] [Amber16]"cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" Scott Le Grand
- [AMBER] Unstable umbrella simulation with Amber16 in GTX1080 kurisaki
- Re: [AMBER] reference or custom GPUs? Ross Walker
- Re: [AMBER] Amber Error David Case
- [AMBER] How to use Amber GAFF force field for methylated DNA MINGREN SHEN
- Re: [AMBER] understanding results Carlos Romero
- [AMBER] calculation of the binding energy in amber 12 or 14 Saikat Pal
Friday, 19 May 2017
- [AMBER] GAFF parameters in amber16 and amber14 Meiting Wang
- Re: [AMBER] GAFF parameters in amber16 and amber14 Hannes Loeffler
- [AMBER] Input case causing NaN in sander (and possibly pmemd) (Ambertools17) Åke Sandgren
- Re: [AMBER] How to use Amber GAFF force field for methylated DNA Hannes Loeffler
- [AMBER] mdgx configuration sampling CA gmail
- Re: [AMBER] mdgx configuration sampling David Cerutti
- Re: [AMBER] cpptraj nastruct local helical vectors? Daniel Roe
- [AMBER] Distance based mask and reference Marion, Antoine
- Re: [AMBER] mdgx configuration sampling David Cerutti
- [AMBER] A9 tutorial analyse.sh problem Robert Wohlhueter
- Re: [AMBER] A9 tutorial analyse.sh problem Hai Nguyen
- Re: [AMBER] A9 tutorial analyse.sh problem Hai Nguyen
Saturday, 20 May 2017
- [AMBER] NetCDF error: Invalid argument xu qingliang
- Re: [AMBER] Distance based mask and reference David Case
- Re: [AMBER] calculation of the binding energy in amber 12 or 14 David A Case
- Re: [AMBER] A9 tutorial analyse.sh problem David Case
- Re: [AMBER] Distance based mask and reference Marion, Antoine
- Re: [AMBER] A9 tutorial analyse.sh problem Robert Wohlhueter
- Re: [AMBER] Query regarding energy calcuation using 3D-RISM Vertika Gautam
- Re: [AMBER] Query regarding energy calcuation using 3D-RISM David Case
- Re: [AMBER-Developers] [AMBER] A9 tutorial analyse.sh problem David Case
- Re: [AMBER] NetCDF error: Invalid argument David Case
Sunday, 21 May 2017
- Re: [AMBER] A9 tutorial analyse.sh problem Robert Wohlhueter
- [AMBER] Unable to view the box coordinates in VMD Ramin Salimi
- Re: [AMBER] Unable to view the box coordinates in VMD David Case
- Re: [AMBER] Unstable umbrella simulation with Amber16 in GTX1080 David Case
- Re: [AMBER] Unable to view the box coordinates in VMD Ramin Salimi
- [AMBER] NetCDF error: Invalid argument xu qingliang
Monday, 22 May 2017
- Re: [AMBER] mdgx configuration sampling CA gmail
- [AMBER] Minimisation of a complex Nikita Devnarain
- Re: [AMBER] Minimisation of a complex Bill Ross
- Re: [AMBER] Minimisation of a complex Nikita Devnarain
- Re: [AMBER] Minimisation of a complex Bill Ross
- Re: [AMBER] Minimisation of a complex Nikita Devnarain
- [AMBER] Wrong Quotation marks in Manual in several examplecodes Johannes Kalliauer
- [AMBER] Regarding Native Contacts Suchetana Gupta
- [AMBER] Which Linux distro for Amber16? Hadházi Ádám
- Re: [AMBER] Unable to view the box coordinates in VMD David Case
- [AMBER] MD Simulation of chemical complex ruqaiya khalil
- Re: [AMBER] Regarding Native Contacts Daniel Roe
- Re: [AMBER] NetCDF error: Invalid argument Daniel Roe
- Re: [AMBER] sander API data structure Brent Krueger
- Re: [AMBER] Unable to view the box coordinates in VMD Ramin Salimi
- Re: [AMBER] sander API data structure Hai Nguyen
- Re: [AMBER] NetCDF error: Invalid argument David Case
Tuesday, 23 May 2017
- Re: [AMBER] AMBER Digest, Vol 1932, Issue 1 Garima Singh
- Re: [AMBER] AMBER Digest, Vol 1932, Issue 1 Elvis Martis
- [AMBER] Virial and Kinetic energy Iain Bethune
- [AMBER] .prmtop file not saved Shafaq Muzammal
- [AMBER] Installation of AMBER 16 Vidhya Srivatsan
- Re: [AMBER] Installation of AMBER 16 Nhai
- Re: [AMBER] Installation of AMBER 16 Hai Nguyen
- [AMBER] Libgfortran error during amber tools install Van Rompaey Dries
- Re: [AMBER] Libgfortran error during amber tools install Hai Nguyen
- Re: [AMBER] .prmtop file not saved David Case
- Re: [AMBER] Libgfortran error during amber tools install David Case
- Re: [AMBER] Libgfortran error during amber tools install Hai Nguyen
- Re: [AMBER] Which Linux distro for Amber16? Hai Nguyen
- Re: [AMBER] Wrong Quotation marks in Manual in several examplecodes Hai Nguyen
- Re: [AMBER] Which Linux distro for Amber16? Jason Swails
- Re: [AMBER] Which Linux distro for Amber16? Bill Ross
- Re: [AMBER] calculation of the binding energy in amber 12 or 14 Saikat Pal
Wednesday, 24 May 2017
- [AMBER] . Re: NetCDF error: Invalid argument (David Case) xu qingliang
- [AMBER] Translate the center of mass of the protein to the origin (0, 0, 0) Meng Wu
- [AMBER] Error while upgrading to AmberTools 17 Chetna Tyagi
- [AMBER] finding number of atoms within a radius Debodyuti Dutta
- Re: [AMBER] finding number of atoms within a radius Elvis Martis
- Re: [AMBER] Error while upgrading to AmberTools 17 Hai Nguyen
- Re: [AMBER] Translate the center of mass of the protein to the origin (0, 0, 0) Daniel Roe
- [AMBER] Reg residue selection in trajectory Vidhya Srivatsan
- Re: [AMBER] Reg residue selection in trajectory Irfan Alibay
- Re: [AMBER] Reg residue selection in trajectory Vidhya Srivatsan
- Re: [AMBER] . Re: NetCDF error: Invalid argument (David Case) David Case
- [AMBER] AMBER error Neha Gandhi
- Re: [AMBER] AMBER error Bill Ross
Thursday, 25 May 2017
- Re: [AMBER] Error while upgrading to AmberTools 17 Chetna Tyagi
- Re: [AMBER] Error while upgrading to AmberTools 17 Hai Nguyen
- Re: [AMBER] AMBER error David Case
- Re: [AMBER] calculation of the binding energy in amber 12 or 14 David Case
- Re: [AMBER] MD Simulation of chemical complex David Case
- Re: [AMBER] AMBER error Neha Gandhi
Friday, 26 May 2017
- [AMBER] amino-cyclopropyl parameters Loris Moretti
- [AMBER] add ligand parameters Loris Moretti
- Re: [AMBER] add ligand parameters Bill Ross
- Re: [AMBER] add ligand parameters Loris Moretti
- Re: [AMBER] add ligand parameters Bill Ross
- Re: [AMBER] add ligand parameters Brent Krueger
- Re: [AMBER] amino-cyclopropyl parameters Thakur, Abhishek
- [AMBER] cpptraj GIST Gabriel Jara
- Re: [AMBER] cpptraj GIST Daniel Roe
Saturday, 27 May 2017
- [AMBER] random coil in the protein secondary structure analysis leila karami
- [AMBER] Question about RMSD "jumps" Ly, Thu Ngoc Anh
- Re: [AMBER] Question about RMSD "jumps" Bill Ross
- [AMBER] Spherical flat bottom restraint M. Wong
Sunday, 28 May 2017
- [AMBER] Fwd: Error while preparing docked complex for minimization NADIA RAHMAH
- Re: [AMBER] Fwd: Error while preparing docked complex for minimization Elvis Martis
- [AMBER] MMGBSA energy decomposition per frame Thomas Evangelidis
- Re: [AMBER] Spherical flat bottom restraint David Case
- Re: [AMBER] Fwd: Error while preparing docked complex for minimization David Case
- Re: [AMBER] Fwd: Error while preparing docked complex for minimization Bill Ross
Monday, 29 May 2017
- [AMBER] Water Geometry in SPCBOX Inconsistent with Literatures Changhao Wang
- Re: [AMBER] Water Geometry in SPCBOX Inconsistent with Literatures David Cerutti
- [AMBER] RESP charge for protonated cytosine ribonucleotide xuzhh
- [AMBER] KeyError: 'A' (MCPB.py) Sushi Shilpa
- [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial Nikolay N. Kuzmich
- [AMBER] Wrong quotation marks in manual David Case
- Re: [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial David Case
- Re: [AMBER] possible bug for reading &qmmm after &lmod David Case
- Re: [AMBER] Input case causing NaN in sander (and possibly pmemd) (Ambertools17) David Case
- Re: [AMBER] RESP charge for protonated cytosine ribonucleotide David Case
- Re: [AMBER] convergence question about xmin David Case
- Re: [AMBER] Input case causing NaN in sander (and possibly pmemd) (Ambertools17) Åke Sandgren
- Re: [AMBER] Amber16 configure: error: could not find mpi library for --enable-mpi Lucas
- Re: [AMBER] Fwd: Error while preparing docked complex for minimization NADIA RAHMAH
- Re: [AMBER] Input case causing NaN in sander (and possibly pmemd) (Ambertools17) David Case
- Re: [AMBER] Amber16 configure: error: could not find mpi library for --enable-mpi David Case
- [AMBER] fcc_metals.lib not found Sohag Biswas
Tuesday, 30 May 2017
- Re: [AMBER] .prmtop file not saved Shafaq Muzammal
- Re: [AMBER] amino-cyclopropyl parameters Loris Moretti
- Re: [AMBER] add ligand parameters Loris Moretti
- [AMBER] No Torsion terms sylvester kisembo
- Re: [AMBER] No Torsion terms Elvis Martis
- Re: [AMBER] amino-cyclopropyl parameters David A Case
- Re: [AMBER] random coil in the protein secondary structure analysis Daniel Roe
- [AMBER] external electric field in Amber 16 michal biler
- Re: [AMBER] external electric field in Amber 16 Carlos Simmerling
- Re: [AMBER] MMGBSA energy decomposition per frame Jason Swails
- Re: [AMBER] Water Geometry in SPCBOX Inconsistent with Literatures Chris Moth
- Re: [AMBER] KeyError: 'A' (MCPB.py) Pengfei Li
- Re: [AMBER] fcc_metals.lib not found Pengfei Li
- Re: [AMBER] external electric field in Amber 16 michal biler
- Re: [AMBER] external electric field in Amber 16 Bill Ross
- [AMBER] Citation for frcmod.parmbsc0, frcmod.ionsjc_tip3p Ramin Salimi
- Re: [AMBER] Citation for frcmod.parmbsc0, frcmod.ionsjc_tip3p Saeed Izadi
- Re: [AMBER] KeyError: 'A' (MCPB.py) Sushi Shilpa
Wednesday, 31 May 2017
- Re: [AMBER] amino-cyclopropyl parameters Loris Moretti
- Re: [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial Nikolay N. Kuzmich
- [AMBER] Antechamber can't transform Gaussian output file into *.mol2 Nikolay N. Kuzmich
- Re: [AMBER] Antechamber can't transform Gaussian output file into *.mol2 Bill Ross
- Re: [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial David A Case
- Re: [AMBER] amino-cyclopropyl parameters David A Case
- Re: [AMBER] Citation for frcmod.parmbsc0, frcmod.ionsjc_tip3p David A Case
- Re: [AMBER] Citation for frcmod.parmbsc0, frcmod.ionsjc_tip3p Ramin Salimi
- Re: [AMBER] cpptraj GIST Tom Kurtzman
- [AMBER] High pressure fluctuation in isothermal-isobaric ensemble Ramin Salimi
- Re: [AMBER] Antechamber can't transform Gaussian output file into *.mol2 Scott Brozell
- Re: [AMBER] High pressure fluctuation in isothermal-isobaric ensemble Daniel Roe
- Re: [AMBER] external electric field in Amber 16 michal biler
- Re: [AMBER] KeyError: 'A' (MCPB.py) Pengfei Li
- Re: [AMBER] external electric field in Amber 16 Bill Ross
- [AMBER] Input case causing NaN in sander David Case

Last message date: Wed May 31 2017 - 19:30:03 PDT
Archived on: Fri Apr 26 2024 - 05:55:35 PDT

Amber Archive May 2017 by date