Amber Archive Apr 2015: by date

Tuesday, 31 March 2015
- Re: [AMBER] Multiple MEPs option in R.E.D tools Yip Yew Mun
- Re: [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files Himanshu Joshi
- Re: [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files Himanshu Joshi
- [AMBER] 发送给你的文件 chemjxn
- [AMBER] MCPB subprogram problem chemjxn
Wednesday, 1 April 2015
- Re: [AMBER] Multiple MEPs option in R.E.D tools Hannes Loeffler
- [AMBER] New Force Field Jason Swails
- Re: [AMBER] New Force Field Adrian Roitberg
- Re: [AMBER] New Force Field Jason Swails
- Re: [AMBER] New Force Field Jiri Sponer
- Re: [AMBER] Help regarding appropriate analysis for correlated motion using cpptraj Jason Swails
- Re: [AMBER] New Force Field Alessandro Contini
- Re: [AMBER] New Force Field Peter Kekenes-Huskey
- Re: [AMBER] MMPBSA error Abhishek TYAGI
- Re: [AMBER] New Force Field Carlos Simmerling
- Re: [AMBER] New Force Field abdennour braka
- Re: [AMBER] New Force Field Alessandro Contini
- Re: [AMBER] New Force Field Daniel Roe
- Re: [AMBER] MMPBSA error Daniel Roe
- Re: [AMBER] New Force Field Carlos Simmerling
- Re: [AMBER] Help regarding appropriate analysis for correlated motion using cpptraj Kshatresh Dutta Dubey
- Re: [AMBER] New Force Field James Maier
- Re: [AMBER] New Force Field sribone.fcq.unc.edu.ar
- Re: [AMBER] Help regarding appropriate analysis for correlated motion using cpptraj Jason Swails
- Re: [AMBER] Help regarding appropriate analysis for correlated motion using cpptraj Kshatresh Dutta Dubey
- Re: [AMBER] MCPB subprogram problem Pengfei Li
- [AMBER] error **** in output file with wrapping first molecule on GPU Quynh Vo
Thursday, 2 April 2015
- [AMBER] Error while running MMPBSA Shreeramesh
- Re: [AMBER] error **** in output file with wrapping first molecule on GPU Gerald Monard
- Re: [AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA psu4.uic.edu
- Re: [AMBER] Multiple MEPs option in R.E.D tools FyD
- Re: [AMBER] Multiple MEPs option in R.E.D tools FyD
- Re: [AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA Gerald Monard
- [AMBER] Free energy calculation of ligand binding energy: Thermodynamic integration - long range dispersion correction - recalculate trajectory with different potential vladimir.palivec.marge.uochb.cas.cz
- Re: [AMBER] Free energy calculation of ligand binding energy: Thermodynamic integration - long range dispersion correction - recalculate trajectory with different potential Hannes Loeffler
- Re: [AMBER] Restrained MD James Starlight
- Re: [AMBER] Error while running MMPBSA Jason Swails
- [AMBER] Build long polymer from the monomer using Xleap James Starlight
- [AMBER] mmbsa.py issue with the complex.parmtop James Starlight
- Re: [AMBER] Build long polymer from the monomer using Xleap Karl Kirschner
- Re: [AMBER] Build long polymer from the monomer using Xleap James Starlight
- Re: [AMBER] Build long polymer from the monomer using Xleap Karl Kirschner
- Re: [AMBER] Error while running MMPBSA Shreeramesh
- [AMBER] mmbsa.py issue with the complex.parmtop Kenneth Huang
- Re: [AMBER] Error while running MMPBSA Kenneth Huang
- Re: [AMBER] mmbsa.py issue with the complex.parmtop James Starlight
- Re: [AMBER] Error while running MMPBSA Shreeramesh
- Re: [AMBER] Error while running MMPBSA Kenneth Huang
- Re: [AMBER] mmbsa.py issue with the complex.parmtop James Starlight
- Re: [AMBER] Error while running MMPBSA Bill Ross
- Re: [AMBER] mmbsa.py issue with the complex.parmtop Kenneth Huang
- [AMBER] Sander QMMM Bomb Problem Gulsevin,Alican
- Re: [AMBER] error **** in output file with wrapping first molecule on GPU Quynh Vo
- Re: [AMBER] error **** in output file with wrapping first molecule on GPU Jason Swails
- [AMBER] FW: amber14 errors IBRAHIM M ABDELRADY
- Re: [AMBER] error **** in output file with wrapping first molecule on GPU Jason Swails
- Re: [AMBER] FW: amber14 errors Jason Swails
- Re: [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12 Brian Radak
- Re: [AMBER] amber14 errors Novosielski, Ryan
- [AMBER] Lipid Conversion from Charmm PDB to Lipid14 PDB Wong, Sook (NIH/NCATS) [V]
- Re: [AMBER] Lipid Conversion from Charmm PDB to Lipid14 PDB Daniel Roe
- Re: [AMBER] FW: amber14 errors IBRAHIM M ABDELRADY
- Re: [AMBER] Lipid Conversion from Charmm PDB to Lipid14 PDB Wong, Sook (NIH/NCATS) [V]
- Re: [AMBER] Lipid Conversion from Charmm PDB to Lipid14 PDB Wong, Sook (NIH/NCATS) [V]
- Re: [AMBER] FW: amber14 errors Jason Swails
- Re: [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12 Jason Swails
- Re: [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12 Brian Radak
Friday, 3 April 2015
- Re: [AMBER] Error while running MMPBSA Shreeramesh
- Re: [AMBER] mmbsa.py issue with the complex.parmtop James Starlight
- Re: [AMBER] error **** in output file with wrapping first molecule on GPU Gerald Monard
- Re: [AMBER] mmbsa.py issue with the complex.parmtop James Starlight
- Re: [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12 Jason Swails
- Re: [AMBER] Error while running MMPBSA Kenneth Huang
- Re: [AMBER] mmbsa.py issue with the complex.parmtop Kenneth Huang
- [AMBER] MMPBSA issues with ff12SB Neha Gandhi
- Re: [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12 Gerald Monard
- Re: [AMBER] MMPBSA issues with ff12SB Ray Luo, Ph.D.
- [AMBER] Trouble recomputing aMD boost from amdlog/mdout Brian Radak
- Re: [AMBER] error **** in output file with wrapping first molecule on GPU Gerald Monard
- Re: [AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA psu4.uic.edu
- Re: [AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA Ross Walker
- Re: [AMBER] MMPBSA issues with ff12SB Neha Gandhi
- Re: [AMBER] MMPBSA issues with ff12SB Ray Luo, Ph.D.
- Re: [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files Ross Walker
Saturday, 4 April 2015
- [AMBER] MMPBSA.py.MPI Installation Failure Laura Tociu
- [AMBER] Question Regarding reduce function of Antechamber Ziheng Wang
Sunday, 5 April 2015
- Re: [AMBER] Question Regarding reduce function of Antechamber David A Case
- [AMBER] The Meaning of Some Parameters wjli
- Re: [AMBER] The Meaning of Some Parameters Carlos Simmerling
- [AMBER] barosts command in amber 12 Chris Gaughan
- Re: [AMBER] Question Regarding reduce function of Antechamber Ziheng Wang
- Re: [AMBER] barosts command in amber 12 Jason Swails
- Re: [AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA psu4.uic.edu
- Re: [AMBER] Question Regarding reduce function of Antechamber David A Case
Monday, 6 April 2015
- [AMBER] query sanjaykumar.imtech.res.in
- Re: [AMBER] mmbsa.py issue with the complex.parmtop James Starlight
- Re: [AMBER] mmbsa.py issue with the complex.parmtop James Starlight
- Re: [AMBER] mmbsa.py issue with the complex.parmtop Kenneth Huang
- Re: [AMBER] mmbsa.py issue with the complex.parmtop Kenneth Huang
- Re: [AMBER] mmbsa.py issue with the complex.parmtop James Starlight
- Re: [AMBER] mmbsa.py issue with the complex.parmtop Kenneth Huang
- Re: [AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA Ross Walker
- [AMBER] Radial distribution function (RDF) for sugars in disaccharides Vijay Achari
- Re: [AMBER] MMPBSA error Abhishek TYAGI
- Re: [AMBER] MMPBSA error Abhishek TYAGI
- Re: [AMBER] MMPBSA error Jason Swails
- Re: [AMBER] MMPBSA error Daniel Roe
- [AMBER] REGARDING ATOM TYPE ERROR Swithin Hanosh
- Re: [AMBER] Build long polymer from the monomer using Xleap FyD
- Re: [AMBER] query FyD
- [AMBER] The force field used in MCPB wjli
Tuesday, 7 April 2015
- [AMBER] typo error in the amber14 manual Vijay Achari
- [AMBER] The Stand Model in MCPB wjli
- Re: [AMBER] query sanjaykumar.imtech.res.in
- [AMBER] error generating P450 prmtop incrd file Vaibhav Dixit
- Re: [AMBER] typo error in the amber14 manual David A Case
- Re: [AMBER] REGARDING ATOM TYPE ERROR Jason Swails
- Re: [AMBER] error generating P450 prmtop incrd file David A Case
- Re: [AMBER] Restrained MD James Starlight
- Re: [AMBER] mmbsa.py issue with the complex.parmtop James Starlight
- Re: [AMBER] error generating P450 prmtop incrd file Vaibhav Dixit
- Re: [AMBER] error generating P450 prmtop incrd file Jason Swails
- [AMBER] potential issue with energy drift Steven Ramsey
- Re: [AMBER] Radial distribution function (RDF) for sugars in disaccharides Daniel Roe
- Re: [AMBER] Restrained MD Daniel Roe
- Re: [AMBER] error generating P450 prmtop incrd file Daniel Roe
- Re: [AMBER] error generating P450 prmtop incrd file Mark Williamson
- Re: [AMBER] Restrained MD James Starlight
- [AMBER] Calculating protein center of mass (COM) using vector command George Green
- Re: [AMBER] The force field used in MCPB Pengfei Li
- [AMBER] FW: TLEAP Fatal Error Wong, Sook (NIH/NCATS) [V]
- Re: [AMBER] The Stand Model in MCPB Pengfei Li
- Re: [AMBER] Calculating protein center of mass (COM) using vector command Daniel Roe
- Re: [AMBER] MMPBSA.py.MPI Installation Failure Jason Swails
- Re: [AMBER] Calculating protein center of mass (COM) using vector command George Green
- Re: [AMBER] FW: TLEAP Fatal Error Jason Swails
- Re: [AMBER] The force field used in MCPB Carlos Simmerling
- Re: [AMBER] FW: TLEAP Fatal Error Wong, Sook (NIH/NCATS) [V]
- Re: [AMBER] The force field used in MCPB Pengfei Li
- [AMBER] COM distance restraints and pmemd.cuda Ilyas Yildirim
- Re: [AMBER] COM distance restraints and pmemd.cuda David A Case
- [AMBER] Possible bug in nativecontacts command of cpptraj (v14)? Samuel Bowerman
- [AMBER] Boltzman Weights from MD trajectory Emilio Angelina
- Re: [AMBER] Boltzman Weights from MD trajectory Jason Swails
- Re: [AMBER] Possible bug in nativecontacts command of cpptraj (v14)? Daniel Roe
- [AMBER] Energy drift issue Steven Ramsey
- [AMBER] Error message in Amber14 tutorial A16 Michael Shokhen
- Re: [AMBER] Energy drift issue Jason Swails
- Re: [AMBER] Boltzman Weights from MD trajectory Emilio Angelina
- Re: [AMBER] Possible bug in nativecontacts command of cpptraj (v14)? Samuel Bowerman
- Re: [AMBER] COM distance restraints and pmemd.cuda Ilyas Yildirim
- [AMBER] Error in tutorial A16, Amber 14 Michael Shokhen
Wednesday, 8 April 2015
- [AMBER] AHTECHAMBER - G09 Sanja Zivanovic
- Re: [AMBER] AHTECHAMBER - G09 Ayesha Fatima
- [AMBER] defining residues in steered molecular dynamics Ayesha Fatima
- Re: [AMBER] error generating P450 prmtop incrd file Vaibhav Dixit
- Re: [AMBER] defining residues in steered molecular dynamics Sourav Purohit
- [AMBER] Visualization of the MMGBSA per-residue decomposition James Starlight
- Re: [AMBER] error generating P450 prmtop incrd file Jason Swails
- Re: [AMBER] error generating P450 prmtop incrd file Jason Swails
- [AMBER] xleap Menu bar problems Pierre Bertin
- Re: [AMBER] Error in tutorial A16, Amber 14 Benjamin D Madej
- [AMBER] MMBP(GB)SA free energy decomposition error: sander failed with prmtop maryam azimzadehirani
- Re: [AMBER] MMPBSA error Abhishek TYAGI
- Re: [AMBER] MMBP(GB)SA free energy decomposition error: sander failed with prmtop Kenneth Huang
- Re: [AMBER] MMPBSA.py.MPI Installation Failure Laura Tociu
Thursday, 9 April 2015
- Re: [AMBER] FW: TLEAP Fatal Error FyD
- Re: [AMBER] error generating P450 prmtop incrd file Vaibhav Dixit
- Re: [AMBER] Error in tutorial A16, Amber 14 Michael Shokhen
- [AMBER] larger bonds between protein atoms Vaibhav Dixit
- Re: [AMBER] xleap Menu bar problems Jason Swails
- Re: [AMBER] larger bonds between protein atoms Jason Swails
- Re: [AMBER] MMPBSA error Jason Swails
- Re: [AMBER] larger bonds between protein atoms David A Case
- Re: [AMBER] MMPBSA error Daniel Roe
- Re: [AMBER] larger bonds between protein atoms Vaibhav Dixit
- [AMBER] Problem with MMPBSA.py.MPI for nmode Sofia Vasilakaki
- Re: [AMBER] Problem with MMPBSA.py.MPI for nmode Kenneth Huang
- Re: [AMBER] Problem with MMPBSA.py.MPI for nmode Sofia Vasilakaki
- Re: [AMBER] xleap Menu bar problems Pierre Bertin
- Re: [AMBER] Error in tutorial A16, Amber 14 Benjamin D Madej
- [AMBER] a question for hydrocarbons simulation using amber FF Nahid Khiabani
- [AMBER] Organic solvent from imported molecule (e.g. : nitric acid) Pierre Bertin
- [AMBER] How to use the mmpbsa.py to calcualte the free energy of a modified protein ? windy
- Re: [AMBER] MMPBSA error Abhishek TYAGI
- [AMBER] Diffusion constant calculation pooja chahal
Friday, 10 April 2015
- [AMBER] Force Field Parameters for Monoamino Acids at acidic and basic conditions? Alain Chaumont
- Re: [AMBER] Organic solvent from imported molecule (e.g. : nitric acid) Karl Kirschner
- Re: [AMBER] Force Field Parameters for Monoamino Acids at acidic and basic conditions? Gerald Monard
- Re: [AMBER] How to use the mmpbsa.py to calcualte the free energy of a modified protein ? Jason Swails
- Re: [AMBER] Force Field Parameters for Monoamino Acids at acidic and basic conditions? Jason Swails
- Re: [AMBER] MMPBSA error Jason Swails
- [AMBER] MMPBSA on NAMD DCD Trajectories Ahmed Ezat
- Re: [AMBER] Build long polymer from the monomer using Xleap James Starlight
- Re: [AMBER] MMPBSA on NAMD DCD Trajectories Jason Swails
- Re: [AMBER] MMPBSA on NAMD DCD Trajectories Ahmed Ezat
- [AMBER] Problem with MMPBSA.py.MPI for nmode Kenneth Huang
- [AMBER] cpptraj write data from runanalysis Gard Nelson
- Re: [AMBER] cpptraj write data from runanalysis Daniel Roe
- [AMBER] Unsupported CUDA version 7.0 detected. Emilio Angelina
- Re: [AMBER] Unsupported CUDA version 7.0 detected. Jason Swails
- Re: [AMBER] Unsupported CUDA version 7.0 detected. Emilio Angelina
- Re: [AMBER] Unsupported CUDA version 7.0 detected. Ross Walker
- Re: [AMBER] Problem with MMPBSA.py.MPI for nmode Sofia Vasilakaki
- Re: [AMBER] cpptraj write data from runanalysis Gard Nelson
- [AMBER] Invitation to Computational Chemical Biology Conference (Aug 6th to 9th 2015), Cairns, Australia (http://tinyurl.com/nyblv7o) Ross Walker
- [AMBER] Does atomicflut byres report the fluctuations of the residue CM? Jose Borreguero
- [AMBER] intercalations Arjun Sharma
- [AMBER] Bad atom Type in MMPBSA.py wjli
- [AMBER] Quasi-harmonic Entropy Calculated using MMPBSA.py Laura Tociu
- Re: [AMBER] How to use the mmpbsa.py to calcualte the free energy of a modified protein ? windy
Saturday, 11 April 2015
- [AMBER] a question for hydrocarbons simulation using amber FF Nahid Khiabani
- Re: [AMBER] Bad atom Type in MMPBSA.py Kenneth Huang
- [AMBER] error in minimization Carlos Romero
- [AMBER] Error Adnan Gulzar
- Re: [AMBER] Problem with MMPBSA.py.MPI for nmode Kenneth Huang
- [AMBER] Amino acid as ligand Dhiraj Srivastava
- Re: [AMBER] Problem with MMPBSA.py.MPI for nmode Jason Swails
- Re: [AMBER] Amino acid as ligand Jason Swails
- Re: [AMBER] error in minimization Bill Ross
- Re: [AMBER] Quasi-harmonic Entropy Calculated using MMPBSA.py Jason Swails
- Re: [AMBER] error in minimization Carlos Romero
- [AMBER] 回复：Re: Bad atom Type in MMPBSA.py wjli
Sunday, 12 April 2015
- Re: [AMBER] Bad atom Type in MMPBSA.py wjli
- [AMBER] a question for hydrocarbons simulation using amber FF Nahid Khiabani
- Re: [AMBER] a question for hydrocarbons simulation using amber FF hannes.loeffler.stfc.ac.uk
- Re: [AMBER] a question for hydrocarbons simulation using amber FF Nahid Khiabani
- Re: [AMBER] a question for hydrocarbons simulation using amber FF Marc van der Kamp
- Re: [AMBER] a question for hydrocarbons simulation using amber FF Nahid Khiabani
- Re: [AMBER] intercalations David A Case
- Re: [AMBER] a question for hydrocarbons simulation using amber FF David A Case
- Re: [AMBER] error in minimization David A Case
- Re: [AMBER] Error David A Case
- Re: [AMBER] a question for hydrocarbons simulation using amber FF David A Case
- Re: [AMBER] a question for hydrocarbons simulation using amber FF Nahid Khiabani
- Re: [AMBER] error in minimization Carlos Romero
- Re: [AMBER] intercalations Bill Ross
- Re: [AMBER] error in minimization Bill Ross
- [AMBER] Arrangement of molecules in 3D packed state jacob wick
- Re: [AMBER] error in minimization Carlos Romero
- Re: [AMBER] Bad atom Type in MMPBSA.py Kenneth Huang
- Re: [AMBER] error in minimization Bill Ross
- Re: [AMBER] error in minimization Carlos Romero
- Re: [AMBER] Arrangement of molecules in 3D packed state Bill Ross
- Re: [AMBER] Arrangement of molecules in 3D packed state David A Case
- Re: [AMBER] error in minimization David A Case
- Re: [AMBER] error in minimization Carlos Romero
- Re: [AMBER] error in minimization Bill Ross
Monday, 13 April 2015
- [AMBER] Mmgbsa decomposition James Starlight
- Re: [AMBER] error in minimization Vaibhav Dixit
- Re: [AMBER] error in minimization David A Case
- [AMBER] re： Bad atom Type in MMPBSA.py wjli
- [AMBER] AMBER parametrization questions Jeffrey Teillet
- Re: [AMBER] error in minimization Carlos Romero
- [AMBER] Charmm force field parameters in Amber anu chandra
- Re: [AMBER] AMBER parametrization questions Carlos Simmerling
- Re: [AMBER] error in minimization Jason Swails
- Re: [AMBER] Charmm force field parameters in Amber Jason Swails
- [AMBER] is it possible to output the trajectory of the center of mass of the residues? Jose Borreguero
- Re: [AMBER] Diffusion constant calculation Daniel Roe
- Re: [AMBER] Does atomicflut byres report the fluctuations of the residue CM? Daniel Roe
- Re: [AMBER] Does atomicflut byres report the fluctuations of the residue CM? Jose Borreguero
- Re: [AMBER] is it possible to output the trajectory of the center of mass of the residues? Daniel Roe
- Re: [AMBER] error in minimization Carlos Romero
- Re: [AMBER] error in minimization Jason Swails
- Re: [AMBER] is it possible to output the trajectory of the center of mass of the residues? Jose Borreguero
- Re: [AMBER] error in minimization Carlos Romero
- Re: [AMBER] error in minimization Jason Swails
- Re: [AMBER] error in minimization Carlos Romero
- Re: [AMBER] re： Bad atom Type in MMPBSA.py Kenneth Huang
- Re: [AMBER] Diffusion constant calculation pooja chahal
Tuesday, 14 April 2015
- [AMBER] hydrogen bond analysis using cpptraj in amber tools 14 Atila Petrosian
- [AMBER] MMPBSA.py error:length mismatch in energy vectors wjli
- [AMBER] Restart file with velocity loic etheve
- Re: [AMBER] Restart file with velocity David A Case
- [AMBER] REGARDING ENERGY MINIMISATION Swithin Hanosh
- Re: [AMBER] hydrogen bond analysis using cpptraj in amber tools 14 Daniel Roe
- Re: [AMBER] Diffusion constant calculation Daniel Roe
- Re: [AMBER] MMPBSA.py error:length mismatch in energy vectors Jason Swails
- Re: [AMBER] REGARDING ENERGY MINIMISATION Jason Swails
- [AMBER] Community network analysis for the Amber trajectories James Starlight
- Re: [AMBER] How to use the mmpbsa.py to calcualte the free energy of a modified protein ? Jason Swails
- Re: [AMBER] error in minimization Carlos Romero
- Re: [AMBER] Community network analysis for the Amber trajectories Daniel Roe
- Re: [AMBER] error in minimization Jason Swails
- Re: [AMBER] error in minimization Carlos Romero
- Re: [AMBER] error in minimization Jason Swails
- Re: [AMBER] Community network analysis for the Amber trajectories James Starlight
- Re: [AMBER] Community network analysis for the Amber trajectories Vlad Cojocaru
- Re: [AMBER] Community network analysis for the Amber trajectories Vlad Cojocaru
- [AMBER] Calculating Cp values from NPT simulations using ptraj Vivek Shankar Bharadwaj
- Re: [AMBER] MMPBSA error Abhishek TYAGI
- [AMBER] Deletion of H atoms from pdb file used for MD simulations muhammad tahir ayub
Wednesday, 15 April 2015
- Re: [AMBER] Deletion of H atoms from pdb file used for MD simulations Ashutosh Shandilya
- Re: [AMBER] Deletion of H atoms from pdb file used for MD simulations suma jayakrishnan
- Re: [AMBER] Deletion of H atoms from pdb file used for MD simulations Hannes Loeffler
- Re: [AMBER] Diffusion constant calculation pooja chahal
- [AMBER] REGARDING ENERGY MINIMISATION Swithin Hanosh
- Re: [AMBER] Community network analysis for the Amber trajectories James Starlight
- Re: [AMBER] Deletion of H atoms from pdb file used for MD simulations Sofia Vasilakaki
- Re: [AMBER] REGARDING ENERGY MINIMISATION Jason Swails
- Re: [AMBER] Deletion of H atoms from pdb file used for MD simulations Jason Swails
- Re: [AMBER] REGARDING ENERGY MINIMISATION David A Case
- [AMBER] The influence of parameters in md.in when restart a MD (from rst file) windy
- Re: [AMBER] The influence of parameters in md.in when restart a MD (from rst file) Daniel Roe
- Re: [AMBER] Deletion of H atoms from pdb file used for MD simulations Daniel Roe
- Re: [AMBER] Diffusion constant calculation Daniel Roe
- Re: [AMBER] Diffusion constant calculation pooja chahal
- [AMBER] Error with quasi-harmonic MMPBSA.py calculations Abhishek TYAGI
- Re: [AMBER] Evaluating hydrogen boding lifetime Vijay Achari
Thursday, 16 April 2015
- [AMBER] Alanin scanning MMGBSA.py error: TypeError: not all arguments converted during string formatting maryam azimzadehirani
- Re: [AMBER] Alanin scanning MMGBSA.py error: TypeError: not all arguments converted during string formatting Jason Swails
- Re: [AMBER] Error with quasi-harmonic MMPBSA.py calculations Jason Swails
- [AMBER] Writing out restart files gepaula.web.de
- Re: [AMBER] Writing out restart files Christina Bergonzo
- Re: [AMBER] Writing out restart files Daniel Roe
- Re: [AMBER] Evaluating hydrogen boding lifetime Daniel Roe
- Re: [AMBER] Writing out restart files Jason Swails
- Re: [AMBER] Diffusion constant calculation Daniel Roe
- [AMBER] all in one pc for MD simulation calculations Atila Petrosian
- Re: [AMBER] all in one pc for MD simulation calculations Jason Swails
- [AMBER] NMode Analysis Using Truncated Trajectory Laura Tociu
- Re: [AMBER] deletion of H atoms for pdb file hannes.loeffler.stfc.ac.uk
- Re: [AMBER] deletion of H atoms for pdb file Daniel Roe
- Re: [AMBER] NMode Analysis Using Truncated Trajectory Jason Swails
- Re: [AMBER] NMode Analysis Using Truncated Trajectory Laura Tociu
- Re: [AMBER] Evaluating hydrogen boding lifetime Vijay Achari
- [AMBER] Could anyone tell me how to run targeted MD correctly 肖立
- [AMBER] Carbon nanotube simulation Pierre Bertin
Friday, 17 April 2015
- Re: [AMBER] Carbon nanotube simulation Karl Kirschner
- Re: [AMBER] Alanin scanning MMGBSA.py error: TypeError: not all arguments converted during string formatting maryam azimzadehirani
- [AMBER] ligand-solvent interaction energy Hannes Loeffler
- Re: [AMBER] The influence of parameters in md.in when restart a MD (from rst file) windy
- [AMBER] Batch leap error! Pallavi Mohanty
- Re: [AMBER] Batch leap error! Hannes Loeffler
- Re: [AMBER] Alanin scanning MMGBSA.py error: TypeError: not all arguments converted during string formatting Jason Swails
- Re: [AMBER] Batch leap error! Pallavi Mohanty
- Re: [AMBER] NMode Analysis Using Truncated Trajectory Jason Swails
- Re: [AMBER] Batch leap error! Jason Swails
- Re: [AMBER] Batch leap error! Jason Swails
- Re: [AMBER] Could anyone tell me how to run targeted MD correctly Carlos Simmerling
- Re: [AMBER] ligand-solvent interaction energy Jason Swails
- Re: [AMBER] NMode Analysis Using Truncated Trajectory Laura Tociu
- Re: [AMBER] Batch leap error! hannes.loeffler.stfc.ac.uk
- Re: [AMBER] Batch leap error! Hannes Loeffler
- Re: [AMBER] Batch leap error! Jason Swails
- Re: [AMBER] Carbon nanotube simulation Daniel Roe
- Re: [AMBER] Evaluating hydrogen boding lifetime Daniel Roe
- Re: [AMBER] Error with quasi-harmonic MMPBSA.py calculations Abhishek TYAGI
- Re: [AMBER] Carbon nanotube simulation Pierre Bertin
- Re: [AMBER] Error with quasi-harmonic MMPBSA.py calculations Jason Swails
- Re: [AMBER] Batch leap error! Pallavi Mohanty
- Re: [AMBER] Batch leap error! Hannes Loeffler
- Re: [AMBER] Batch leap error! Hector A. Baldoni
- Re: [AMBER] Could anyone tell me how to run targeted MD correctly 肖立
- Re: [AMBER] Could anyone tell me how to run targeted MD correctly Carlos Simmerling
- Re: [AMBER] Could anyone tell me how to run targeted MD correctly 肖立
- Re: [AMBER] Could anyone tell me how to run targeted MD correctly 肖立
- Re: [AMBER] Evaluating hydrogen boding lifetime Vijay Achari
- [AMBER] How to resolve the problem when amber14 configured with cuda 6.5 金毅
Saturday, 18 April 2015
- Re: [AMBER] How to resolve the problem when amber14 configured with cuda 6.5 Ross Walker
- Re: [AMBER] How to resolve the problem when amber14 configured with cuda 6.5 Jason Swails
- Re: [AMBER] How to resolve the problem when amber14 configured with cuda 6.5 金毅
- Re: [AMBER] How to resolve the problem when amber14 configured with cuda 6.5 金毅
Sunday, 19 April 2015
- [AMBER] Problem regarding PMF curve Shubhadip Das
- Re: [AMBER] How to resolve the problem when amber14 configured with cuda 6.5 Jason Swails
- [AMBER] One chain of protein going out of box Shukla, Saurabh
- [AMBER] Problem in running with steered MD 肖立
Monday, 20 April 2015
- [AMBER] In MMPBSY.py , how to set interval value when large conformation change ? windy
- [AMBER] regarding .prmtop file generation neha chaudhary
- [AMBER] PCA analysis Muthukumaran R
- Re: [AMBER] Problem in running with steered MD Jason Swails
- Re: [AMBER] One chain of protein going out of box Jason Swails
- Re: [AMBER] PCA analysis Jason Swails
- Re: [AMBER] regarding .prmtop file generation Jason Swails
- Re: [AMBER] In MMPBSY.py , how to set interval value when large conformation change ? Jason Swails
- Re: [AMBER] PCA analysis Muthukumaran R
- [AMBER] cpptraj writting box coordinates issue CHAMI F.
- Re: [AMBER] cpptraj writting box coordinates issue Daniel Roe
- Re: [AMBER] cpptraj writting box coordinates issue CHAMI F.
- Re: [AMBER] In MMPBSY.py , how to set interval value when large conformation change ? George Tzotzos
- Re: [AMBER] In MMPBSY.py , how to set interval value when large conformation change ? Jason Swails
Tuesday, 21 April 2015
- Re: [AMBER] Arrangement of molecules in 3D packed state jacob wick
- [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Vaibhav Dixit
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Kenneth Huang
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Vaibhav Dixit
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Daniel Roe
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Vaibhav Dixit
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Vaibhav Dixit
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Sajeewa Pemasinghe
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Vaibhav Dixit
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Sajeewa Pemasinghe
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Hector A. Baldoni
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Jason Swails
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" David A Case
- [AMBER] ATTN needs revision Sanja Zivanovic
- [AMBER] The error occurs when I set radiopt =1 in MMPBSA.py wliu
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Vaibhav Dixit
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Kenneth Huang
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Vaibhav Dixit
- Re: [AMBER] The error occurs when I set radiopt =1 in MMPBSA.py Kenneth Huang
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Jason Swails
- Re: [AMBER] The error occurs when I set radiopt =1 in MMPBSA.py Jason Swails
- Re: [AMBER] Calculating Cp values from NPT simulations using ptraj Daniel Roe
- [AMBER] install Amber 11 and AmberTools 1.5 on CentoS 6.3 Atila Petrosian
- Re: [AMBER] install Amber 11 and AmberTools 1.5 on CentoS 6.3 Jason Swails
- [AMBER] Amber GPU Segmentation fault AJ Venkatakrishnan
- Re: [AMBER] Amber GPU Segmentation fault Ross Walker
- Re: [AMBER] In MMPBSY.py , how to set interval value when large conformation change ? windy
- [AMBER] install Amber 11 and AmberTools 1.5 on CentoS 6.3 Atila Petrosian
Wednesday, 22 April 2015
- Re: [AMBER] In MMPBSY.py , how to set interval value when large conformation change ? Jason Swails
- Re: [AMBER] install Amber 11 and AmberTools 1.5 on CentoS 6.3 Jason Swails
- Re: [AMBER] ATTN needs revision David A Case
- Re: [AMBER] Arrangement of molecules in 3D packed state David A Case
- [AMBER] Any timeline for TI on GPU's? Ucisik, Melek Nihan
- Re: [AMBER] install Amber 11 and AmberTools 1.5 on CentoS 6.3 Atila Petrosian
- Re: [AMBER] install Amber 11 and AmberTools 1.5 on CentoS 6.3 Hai Nguyen
- Re: [AMBER] Any timeline for TI on GPU's? filip fratev
- Re: [AMBER] install Amber 11 and AmberTools 1.5 on CentoS 6.3 Jason Swails
- [AMBER] CENTOS 6.6 :ERROR - INSTALLATION OF AMBERTOOLS14/AMBER14 vitonoja.yahoo.com
- Re: [AMBER] In MMPBSY.py , how to set interval value when large conformation change ? windy
- [AMBER] mcpb problem chemjxn
- [AMBER] AMBER 14 installation problem Sanjib Paul
- Re: [AMBER] Any timeline for TI on GPU's? Ross Walker
Thursday, 23 April 2015
- Re: [AMBER] MMBP(GB)SA free energy decomposition error: sander failed with prmtop maryam azimzadehirani
- Re: [AMBER] Error with quasi-harmonic MMPBSA.py calculations Abhishek TYAGI
- Re: [AMBER] Arrangement of molecules in 3D packed state jacob wick
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram
- Re: [AMBER] CENTOS 6.6 :ERROR - INSTALLATION OF AMBERTOOLS14/AMBER14 Jason Swails
- Re: [AMBER] AMBER 14 installation problem Jason Swails
- Re: [AMBER] Error with quasi-harmonic MMPBSA.py calculations Jason Swails
- Re: [AMBER] MMBP(GB)SA free energy decomposition error: sander failed with prmtop Jason Swails
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails
- Re: [AMBER] The error occurs when I set radiopt =1 in MMPBSA.py wliu
- Re: [AMBER] Problem regarding PMF curve Brian Radak
- Re: [AMBER] AMBER 14 installation problem Sanjib Paul
- Re: [AMBER] mcpb problem Pengfei Li
- Re: [AMBER] Arrangement of molecules in 3D packed state David A Case
- Re: [AMBER] Arrangement of molecules in 3D packed state Pawel Janowski
- [AMBER] Free energy calculation of ligand binding energy: Thermodynamic integration - pmemd - single topology - vdw vladimir.palivec.marge.uochb.cas.cz
- Re: [AMBER] Free energy calculation of ligand binding energy: Thermodynamic integration - pmemd - single topology - vdw hannes.loeffler.stfc.ac.uk
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram
- Re: [AMBER] Arrangement of molecules in 3D packed state jacob wick
- Re: [AMBER] Arrangement of molecules in 3D packed state jacob wick
- [AMBER] water box for steered md amber14 Asmita Gupta
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Vaibhav Dixit
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram
- [AMBER] DNA partial charges in Amber library jacob wick
- Re: [AMBER] DNA partial charges in Amber library Thomas Cheatham
Friday, 24 April 2015
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails
- [AMBER] Simulations at High temperature (425K) Biswa Ranjan Meher
- Re: [AMBER] Simulations at High temperature (425K) Carlos Simmerling
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram
- Re: [AMBER] Simulations at High temperature (425K) David A Case
- Re: [AMBER] Amber GPU Segmentation fault AJ Venkatakrishnan
Saturday, 25 April 2015
- [AMBER] mcpb problem chemjxn
- Re: [AMBER] regarding .prmtop file generation neha chaudhary
- [AMBER] Regarding running to independent simulations Soumendranath Bhakat
- [AMBER] charmmlipid2amber2.py error Gözde YALÇIN
- Re: [AMBER] Free energy calculation of ligand binding energy: Thermodynamic integration - pmemd - single topology - vdw vladimir.palivec.marge.uochb.cas.cz
- [AMBER] Regarding running to independent simulations Kenneth Huang
- Re: [AMBER] charmmlipid2amber2.py error Michele Bonus
- Re: [AMBER] Regarding running to independent simulations David A Case
- Re: [AMBER] Free energy calculation of ligand binding energy: Thermodynamic integration - pmemd - single topology - vdw hannes.loeffler.stfc.ac.uk
- [AMBER] segmentation fault in AmberTool 14.25 MOHD HOMAIDUR RAHMAN
- [AMBER] close contacts in equilibrated structure Asmita Gupta
- Re: [AMBER] mcpb problem Jia Xu
- [AMBER] the vectors of the moment of inertia protein CHAMI F.
- [AMBER] problem with CHAMBER sudipta
- [AMBER] charmmlipid2amber.py error Gözde YALÇIN
- Re: [AMBER] regarding .prmtop file generation Jason Swails
- Re: [AMBER] segmentation fault in AmberTool 14.25 Jason Swails
- Re: [AMBER] close contacts in equilibrated structure Jason Swails
- Re: [AMBER] charmmlipid2amber.py error Jason Swails
- Re: [AMBER] segmentation fault in AmberTool 14.25 Bill Ross
- Re: [AMBER] problem with CHAMBER Jason Swails
- Re: [AMBER] close contacts in equilibrated structure Asmita Gupta
Sunday, 26 April 2015
- Re: [AMBER] Regarding running to independent simulations Soumendranath Bhakat
- [AMBER] mpirun error shahab shariati
- Re: [AMBER] mpirun error Jason Swails
- [AMBER] Quasi-harmonic Approximation Using a Trajectory Stripped of Hydrogens Laura Tociu
- Re: [AMBER] regarding .prmtop file generation neha chaudhary
- [AMBER] Segmentation fault in AmberTool 14.25 MOHD HOMAIDUR RAHMAN
Monday, 27 April 2015
- [AMBER] parameterization Zn2+ with MCPB chemjxn
- Re: [AMBER] regarding .prmtop file generation David A Case
- Re: [AMBER] Segmentation fault in AmberTool 14.25 David A Case
- [AMBER] Questions about T-REMD lipengfei
- Re: [AMBER] Questions about T-REMD Jason Swails
- Re: [AMBER] parameterization Zn2+ with MCPB Pengfei Li
- [AMBER] cpptraj V14.25 issues with old Amber topology files (Amber 11) CHAMI F.
- Re: [AMBER] cpptraj V14.25 issues with old Amber topology files (Amber 11) Jason Swails
- Re: [AMBER] cpptraj V14.25 issues with old Amber topology files (Amber 11) Daniel Roe
- Re: [AMBER] cpptraj V14.25 issues with old Amber topology files (Amber 11) CHAMI F.
- Re: [AMBER] cpptraj V14.25 issues with old Amber topology files (Amber 11) Daniel Roe
- [AMBER] how to run non standard simulation muhammad tahir ayub
- Re: [AMBER] how to run non standard simulation David A Case
- [AMBER] Antechamber Algorithm for Atom Type Robert Molt
- [AMBER] Is there NHE cap in the ff02 library files? Yip Yew Mun
- [AMBER] Fwd: Tleap atom type - template not found Balaji Selvam
- Re: [AMBER] Segmentation fault in AmberTool 14.25 MOHD HOMAIDUR RAHMAN
- Re: [AMBER] Antechamber Algorithm for Atom Type hannes.loeffler.stfc.ac.uk
Tuesday, 28 April 2015
- Re: [AMBER] Quasi-harmonic Approximation Using a Trajectory Stripped of Hydrogens Josh Berryman
- [AMBER] Nmode analysis calculation problem for Implicit simulation. Bajarang Kumbhar
- [AMBER] error in amber installation Atila Petrosian
- Re: [AMBER] Quasi-harmonic Approximation Using a Trajectory Stripped of Hydrogens Hannes Loeffler
- Re: [AMBER] Is there NHE cap in the ff02 library files? David A Case
- Re: [AMBER] Fwd: Tleap atom type - template not found David A Case
- Re: [AMBER] Segmentation fault in AmberTool 14.25 David A Case
- Re: [AMBER] Nmode analysis calculation problem for Implicit simulation. David A Case
- Re: [AMBER] error in amber installation David A Case
- Re: [AMBER] Antechamber Algorithm for Atom Type Robert Molt
- Re: [AMBER] Antechamber Algorithm for Atom Type Hannes Loeffler
- Re: [AMBER] Antechamber Algorithm for Atom Type Robert Molt
- Re: [AMBER] Antechamber Algorithm for Atom Type Jason Swails
- Re: [AMBER] Antechamber Algorithm for Atom Type Hannes Loeffler
- Re: [AMBER] Antechamber Algorithm for Atom Type Hannes Loeffler
- Re: [AMBER] Antechamber Algorithm for Atom Type Jason Swails
- [AMBER] pdbamb gives wrong resnumber Miguel Ángel Mompeán García
- Re: [AMBER] pdbamb gives wrong resnumber Jason Swails
- [AMBER] EGB and EEL Values in MM-GBSA -reg Muthukumaran R
- Re: [AMBER] pdbamb gives wrong resnumber David A Case
- Re: [AMBER] EGB and EEL Values in MM-GBSA -reg Jason Swails
- Re: [AMBER] Quasi-harmonic Approximation Using a Trajectory Stripped of Hydrogens Laura Tociu
- Re: [AMBER] Antechamber Algorithm for Atom Type Robert Molt
- Re: [AMBER] Quasi-harmonic Approximation Using a Trajectory Stripped of Hydrogens Jason Swails
- Re: [AMBER] Quasi-harmonic Approximation Using a Trajectory Stripped of Hydrogens Laura Tociu
Wednesday, 29 April 2015
- Re: [AMBER] charmmlipid2amber.py error Gözde YALÇIN
- [AMBER] dispersion for QM/MM missing parameters Jorgen Simonsen
- [AMBER] The question about how to restart REMD simulation in AMBER12 and Langavin dynamics Wang Moye
- Re: [AMBER] The question about how to restart REMD simulation in AMBER12 and Langavin dynamics Jason Swails
- [AMBER] Query about microsecond long simulation anu chandra
- Re: [AMBER] Query about microsecond long simulation Ross Walker
- Re: [AMBER] Query about microsecond long simulation Ahmed Ezat
- Re: [AMBER] Query about microsecond long simulation Jason Swails
- Re: [AMBER] Query about microsecond long simulation Ahmed Ezat
- Re: [AMBER] Query about microsecond long simulation anu chandra
- Re: [AMBER] Query about microsecond long simulation Jason Swails
- Re: [AMBER] Query about microsecond long simulation David A Case
- Re: [AMBER] Query about microsecond long simulation anu chandra
- Re: [AMBER] Query about microsecond long simulation Robert Molt
- [AMBER] lipid simulation queries Bala subramanian
- Re: [AMBER] Query about microsecond long simulation Bill Ross
- [AMBER] MMPBSA problem with calcium Francesco Gentile
- Re: [AMBER] Query about microsecond long simulation David A Case
- Re: [AMBER] Query about microsecond long simulation Thomas C. Bishop
- Re: [AMBER] Query about microsecond long simulation Dr. Robert Molt Jr.
- Re: [AMBER] Query about microsecond long simulation Andrew Schaub
- [AMBER] restraining in xz coordinates only Samaneh Mesbahi
Thursday, 30 April 2015
- Re: [AMBER] Quasi-harmonic Approximation Using a Trajectory Stripped of Hydrogens Hannes Loeffler
- Re: [AMBER] Query about microsecond long simulation Gustavo Seabra
- Re: [AMBER] Query about microsecond long simulation Ross Walker
- Re: [AMBER] Query about microsecond long simulation David A Case
- Re: [AMBER] Query about microsecond long simulation David A Case
- [AMBER] STRUCTURAL CHANGE AFTER HEATING Swithin Hanosh
- Re: [AMBER] Query about microsecond long simulation anu chandra
- [AMBER] restraining in xz coordinates only Samaneh Mesbahi
- Re: [AMBER] STRUCTURAL CHANGE AFTER HEATING David A Case
- Re: [AMBER] MMPBSA problem with calcium Jason Swails
- Re: [AMBER] Query about microsecond long simulation Jason Swails
- Re: [AMBER] Query about microsecond long simulation Jason Swails
- Re: [AMBER] Query about microsecond long simulation Jonathan Gough
- Re: [AMBER] Query about microsecond long simulation Jason Swails
- Re: [AMBER] Query about microsecond long simulation Jonathan Gough
- Re: [AMBER] restraining in xz coordinates only Jason Swails
- Re: [AMBER] Query about microsecond long simulation Jason Swails
- [AMBER] Bursary deadline, May 15, 2015: Drug Discovery Workshops Milan Thomas Exner
- [AMBER] Bursary deadline, May 15, 2015: Drug Discovery Workshops Canada Thomas Exner
- Re: [AMBER] MMPBSA problem with calcium Francesco Gentile
- Re: [AMBER] MMPBSA problem with calcium Jason Swails

Last message date: Thu Apr 30 2015 - 16:00:02 PDT
Archived on: Fri Nov 15 2024 - 05:55:14 PST

Amber Archive Apr 2015 by date