Amber Archive Dec 2013: by date

Saturday, 30 November 2013
- [AMBER] Does pmemd or pmemd.mpi support center of mass restraint? zhongqiao hu
Sunday, 1 December 2013
- Re: [AMBER] planarity of Trp side chain and improper torsion term Jorge Iulek
- Re: [AMBER] Does pmemd or pmemd.mpi support center of mass restraint? zhongqiao hu
- Re: [AMBER] planarity of Trp side chain and improper torsion term case
- Re: [AMBER] internal geometry restraint Jio M
Monday, 2 December 2013
- [AMBER] SETTING QM ZONE Tanmoy Paul
- Re: [AMBER] internal geometry restraint David A Case
- [AMBER] saveamberparameters problem Saeed Nasiri
- Re: [AMBER] internal geometry restraint Jio M
- [AMBER] Compare the result between pmemd.cuda and pmemd.mpi? X Sun
- Re: [AMBER] Compare the result between pmemd.cuda and pmemd.mpi? Ross Walker
- Re: [AMBER] Compare the result between pmemd.cuda and pmemd.mpi? Jason Swails
- Re: [AMBER] saveamberparameters problem David A Case
- Re: [AMBER] internal geometry restraint David A Case
- Re: [AMBER] PARSE radii and effective radii IN MM/PBSA & MM/GBSA psu4.uic.edu
- Re: [AMBER] PARSE radii and effective radii IN MM/PBSA & MM/GBSA Ray Luo, Ph.D.
- [AMBER] Calculation of NMR relaxation rates Mahendra B Thapa
- [AMBER] zinc parameters Hallel Freedman
Tuesday, 3 December 2013
- Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 Jan-Philip Gehrcke
- [AMBER] AMBER12 test discrepancy Guanglei Cui
- [AMBER] parmed.py setBond Aronica, Pietro
- Re: [AMBER] parmed.py setBond Brian Radak
- Re: [AMBER] parmed.py setBond Aronica, Pietro
- Re: [AMBER] parmed.py setBond Brian Radak
- Re: [AMBER] zinc parameters Hallel Freedman
- Re: [AMBER] parmed.py setBond Aronica, Pietro
- Re: [AMBER] zinc parameters Bill Ross
- Re: [AMBER] zinc parameters Hallel Freedman
- Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 Ray Luo, Ph.D.
- Re: [AMBER] parmed.py setBond Jason Swails
- Re: [AMBER] parmed.py setBond Jason Swails
- [AMBER] How to compile amber12 in AIX UNIX? Mengyuan Zhu
- Re: [AMBER] parmed.py setBond Jason Swails
- Re: [AMBER] parmed.py setBond Aronica, Pietro
- Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 wmsmith.uci.edu
- [AMBER] Restrained MD with COM restraint with PMEMD Mike Limb
- Re: [AMBER] parmed.py setBond Jason Swails
- Re: [AMBER] How to compile amber12 in AIX UNIX? case
- Re: [AMBER] Restrained MD with COM restraint with PMEMD case
- Re: [AMBER] Calculation of NMR relaxation rates case
- Re: [AMBER] How to compile amber12 in AIX UNIX? Mengyuan Zhu
- Re: [AMBER] How to compile amber12 in AIX UNIX? Mengyuan Zhu
- Re: [AMBER] How to compile amber12 in AIX UNIX? Daniel Roe
Wednesday, 4 December 2013
- Re: [AMBER] Restrained MD with COM restraint with PMEMD Mike Limb
- Re: [AMBER] Restrained MD with COM restraint with PMEMD Jason Swails
- [AMBER] nasiri Saeed Nasiri
- Re: [AMBER] nasiri Jason Swails
- Re: [AMBER] Calculation of NMR relaxation rates Daniel Roe
- [AMBER] Keeping an hexamer whole. Julio Dominguez
- Re: [AMBER] Temperature raises abnormally during accelerated MD O Z
- Re: [AMBER] Keeping an hexamer whole. Jason Swails
- Re: [AMBER] Keeping an hexamer whole. Daniel Roe
- Re: [AMBER] zinc parameters Bill Ross
Thursday, 5 December 2013
- [AMBER] Constant pH anurag.dobhal
- [AMBER] RMSF John Smith
- [AMBER] constant pH anurag.dobhal
- Re: [AMBER] constant pH Kshatresh Dutta Dubey
- Re: [AMBER] constant pH David A Case
- Re: [AMBER] RMSF David A Case
- Re: [AMBER] RMSF Jason Swails
- Re: [AMBER] RMSF John Smith
- Re: [AMBER] RMSF Jason Swails
- Re: [AMBER] zinc parameters Hallel Freedman
- Re: [AMBER] RMSF John Smith
- Re: [AMBER] Topology files of homodimer-ligand complex Jason Swails
- Re: [AMBER] RMSF John Smith
- Re: [AMBER] RMSF Jason Swails
- [AMBER] question Zahra Khatti
- Re: [AMBER] question Jason Swails
- Re: [AMBER] question Hamed S. Hayatshahi
- [AMBER] Error in amber12 serial installation in file alltasks_setup.F90:352 Sajeewa Pemasinghe
- [AMBER] Converting Amoeba .xyz for use with Amber Eugene Yedvabny
- Re: [AMBER] Keeping an hexamer whole. Julio Dominguez
- Re: [AMBER] How to compile amber12 in AIX UNIX? Mengyuan Zhu
- [AMBER] When to use semi-anisotropic pressure couplings Vijay Manickam Achari
Friday, 6 December 2013
- [AMBER] Plotting a Dynamic Cross Correlation Map Yip Yew Mun
- [AMBER] anisotropic & semi-anisotropic pressure coupling. Vijay Manickam Achari
- Re: [AMBER] Error in amber12 serial installation in file alltasks_setup.F90:352 David A Case
- Re: [AMBER] Converting Amoeba .xyz for use with Amber David A Case
- [AMBER] ptraj hbond output format Andre C. Stiel
- [AMBER] compile parallel mpi Zahra Khatti
- Re: [AMBER] compile parallel mpi Jason Swails
- [AMBER] Should vdW cutoff distance be system-dependent? yunshi11 .
- Re: [AMBER] Should vdW cutoff distance be system-dependent? David A Case
- Re: [AMBER] Should vdW cutoff distance be system-dependent? Brian Radak
- [AMBER] Using the RED Server Dev. to parameterize a model transition state Kamali Sripathi
- Re: [AMBER] Error in amber12 serial installation in file alltasks_setup.F90:352 Jason Swails
- Re: [AMBER] Converting Amoeba .xyz for use with Amber Jason Swails
- Re: [AMBER] ptraj hbond output format Daniel Roe
Saturday, 7 December 2013
- [AMBER] Anisotropic & semi-anisotropic Vijay Manickam Achari
- Re: [AMBER] Anisotropic & semi-anisotropic Jason Swails
- [AMBER] not getting correct density for N,N-dimethylformamide Sohag Biswas
- Re: [AMBER] not getting correct density for N,N-dimethylformamide FyD
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state FyD
Sunday, 8 December 2013
- Re: [AMBER] ptraj hbond output format André C. Stiel
- Re: [AMBER] ptraj hbond output format Jan-Philip Gehrcke
- [AMBER] Atom Expression in NAB sunita gupta
- Re: [AMBER] Atom Expression in NAB case
- [AMBER] Brookhaven pdb format 闫玉娜
- Re: [AMBER] Brookhaven pdb format Daniel Roe
- Re: [AMBER] Brookhaven pdb format 闫玉娜
- Re: [AMBER] Atom Expression in NAB sunita gupta
- Re: [AMBER] Atom Expression in NAB sunita gupta
Monday, 9 December 2013
- [AMBER] accelerated Molecular dynamics Ibrahim Said
- Re: [AMBER] Atom Expression in NAB Jason Swails
- Re: [AMBER] accelerated Molecular dynamics Jason Swails
- [AMBER] MMPBSA errors ：setting grid spacing larger than solvent probe Fengxue Li
- Re: [AMBER] MMPBSA errors ：setting grid spacing larger than solvent probe Jason Swails
- [AMBER] math operations in cpptraj Andre C. Stiel
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state Kamali Sripathi
- Re: [AMBER] math operations in cpptraj Daniel Roe
- Re: [AMBER] MMPBSA errors ：setting grid spacing larger than solvent probe Ray Luo, Ph.D.
- [AMBER] please tell me why this error is coming while doing the constant pH MD anurag.dobhal
- Re: [AMBER] please tell me why this error is coming while doing the constant pH MD Jason Swails
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state FyD
- [AMBER] Fwd: Re: Using the RED Server Dev. to parameterize a model transition state FyD
- Re: [AMBER] not getting correct density for N,N-dimethylformamide David A Case
- [AMBER] Amber Tools v.13 Silvestre
- Re: [AMBER] Amber Tools v.13 Jason Swails
- [AMBER] Converting Amoeba .xyz for use with Amber Eugene Yedvabny
- Re: [AMBER] Amber Tools v.13 Silvestre
- Re: [AMBER] Converting Amoeba .xyz for use with Amber Eugene Yedvabny
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state Kamali Sripathi
- [AMBER] netcdf compilation error in Amber12 serial installation: Couldn't compile conftest.c Sajeewa Pemasinghe
- Re: [AMBER] netcdf compilation error in Amber12 serial installation: Couldn't compile conftest.c Aldo Segura
- Re: [AMBER] netcdf compilation error in Amber12 serial installation: Couldn't compile conftest.c Jason Swails
- Re: [AMBER] Anisotropic & semi-anisotropic Vijay Manickam Achari
- [AMBER] Does anyone know which parameter controls the wavenumber related to the Helmholtz equation 肖立
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state FyD
Tuesday, 10 December 2013
- [AMBER] sander command Saeed Nasiri
- [AMBER] MMPBSA errors :failed with prmtop Fengxue Li
- [AMBER] capturing free energy landscape anu chandra
- [AMBER] AMBER GPU performance issue Neha Gandhi
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state Kamali Sripathi
- Re: [AMBER] Does anyone know which parameter controls the wavenumber related to the Helmholtz equation wmsmith.uci.edu
- Re: [AMBER] Does anyone know which parameter controls the wavenumber related to the Helmholtz equation 肖立
- Re: [AMBER] MMPBSA errors :failed with prmtop Ray Luo, Ph.D.
- Re: [AMBER] Does anyone know which parameter controls the wavenumber related to the Helmholtz equation wmsmith.uci.edu
- Re: [AMBER] netcdf compilation error in Amber12 serial installation: Couldn't compile conftest.c Sajeewa Pemasinghe
- Re: [AMBER] netcdf compilation error in Amber12 serial installation: Couldn't compile conftest.c Daniel Roe
- Re: [AMBER] AMBER GPU performance issue Jason Swails
- Re: [AMBER] capturing free energy landscape Jason Swails
- Re: [AMBER] capturing free energy landscape Thomas Evangelidis
- Re: [AMBER] capturing free energy landscape Adrian Roitberg
Wednesday, 11 December 2013
- [AMBER] cpptraj output and hbond André C. Stiel
- Re: [AMBER] sander command Jason Swails
- [AMBER] Is there any way I can complete a production run which has been interrupted by a sudden power cut ? Roza M
- [AMBER] Amber QM/MM Fengxue Li
- Re: [AMBER] capturing free energy landscape anu chandra
- Re: [AMBER] Amber QM/MM Brian Radak
- Re: [AMBER] Is there any way I can complete a production run which has been interrupted by a sudden power cut ? Gustavo Seabra
- Re: [AMBER] Amber QM/MM Gustavo Seabra
- [AMBER] runing sander Saeed Nasiri
- [AMBER] Plotting heat maps in AMBER aMD simualtions filip fratev
- Re: [AMBER] Plotting heat maps in AMBER aMD simualtions Brian Radak
- Re: [AMBER] Is there any way I can complete a production run which has been interrupted by a sudden power cut ? Roza M
- Re: [AMBER] Plotting heat maps in AMBER aMD simualtions Jason Swails
- Re: [AMBER] runing sander Jason Swails
- Re: [AMBER] Plotting heat maps in AMBER aMD simualtions filip fratev
- Re: [AMBER] Plotting heat maps in AMBER aMD simualtions Daniel Roe
- [AMBER] cpptraj output and hbond André C. Stiel
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state Kamali Sripathi
- Re: [AMBER] Amber Tools v.13 Silvestre
- Re: [AMBER] Amber Tools v.13 Daniel Roe
- [AMBER] Regarding generating parameters for protein with NAD+ Prema Mallipeddi
- [AMBER] Does anyone knows how to generate an ired vector 肖立
- Re: [AMBER] Does anyone knows how to generate an ired vector Daniel Roe
- Re: [AMBER] Does anyone knows how to generate an ired vector 肖立
- Re: [AMBER] Does anyone knows how to generate an ired vector wmsmith.uci.edu
- Re: [AMBER] Amber Tools v.13 Jason Swails
- Re: [AMBER] Regarding generating parameters for protein with NAD+ case
- Re: [AMBER] Does anyone knows how to generate an ired vector Daniel Roe
- Re: [AMBER] Does anyone knows how to generate an ired vector Daniel Roe
- [AMBER] The use of ansiotropic & semi-anisotropic pressure couplings in bilayer simulation. Vijay Manickam Achari
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state FyD
- Re: [AMBER] Does anyone knows how to generate an ired vector 肖立
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state FyD
- [AMBER] atom-atom contact analysis in PTRAj Pranjal Mahanta
Thursday, 12 December 2013
- [AMBER] I got a error David Chen
- [AMBER] Puzzles about calculating the binding energy of residues Yanyan ZHU
- Re: [AMBER] Amber QM/MM Ross Walker
- [AMBER] Simulation time help Nicole Ippolito
- Re: [AMBER] Simulation time help Adrian Roitberg
- Re: [AMBER] Simulation time help Nicole Ippolito
- Re: [AMBER] Simulation time help Adrian Roitberg
- Re: [AMBER] Simulation time help Nicole Ippolito
- [AMBER] changeLJSingleType problem in parmed.py Hamed S. Hayatshahi
- Re: [AMBER] changeLJSingleType problem in parmed.py Jason Swails
- [AMBER] how to remove the rotational center-of-mass motion ? 张明焜
Friday, 13 December 2013
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state FyD
- [AMBER] MGMS-DS: Molecular Modelling Workshop 2014 in Erlangen, Germany Harald Lanig
- [AMBER] I got a error David Chen
- Re: [AMBER] how to remove the rotational center-of-mass motion ? David A Case
- [AMBER] 3D projection of pairwise-RMSD Sangeetha B
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state Kamali Sripathi
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state FyD
- Re: [AMBER] 3D projection of pairwise-RMSD Daniel Roe
- [AMBER] AmberTools update 22 for CPPTRAJ Daniel Roe
- Re: [AMBER] I got a error Jason Swails
- Re: [AMBER] 3D projection of pairwise-RMSD Sangeetha B
- Re: [AMBER] 3D projection of pairwise-RMSD Adrian Roitberg
- Re: [AMBER] 3D projection of pairwise-RMSD Adrian Roitberg
- Re: [AMBER] 3D projection of pairwise-RMSD Sangeetha B
- Re: [AMBER] 3D projection of pairwise-RMSD David A Case
- [AMBER] error in installing ambertools 1.2 anurag.dobhal
- [AMBER] issues with MMPBSA tutorial/MMPBSA.py Bennion, Brian
- Re: [AMBER] Does pmemd or pmemd.mpi support center of mass restraint? Igor Marques
- Re: [AMBER] Does pmemd or pmemd.mpi support center of mass restraint? Ross Walker
- Re: [AMBER] Converting Amoeba .xyz for use with Amber Eugene Yedvabny
Saturday, 14 December 2013
- [AMBER] Puzzles about calculating binding energy using MMGBSA Yanyan ZHU
- Re: [AMBER] Puzzles about calculating binding energy using MMGBSA Jason Swails
- Re: [AMBER] Converting Amoeba .xyz for use with Amber case
- Re: [AMBER] error in installing ambertools 1.2 case
- [AMBER] Proper Algorithm for GPU? X Sun
- Re: [AMBER] Converting Amoeba .xyz for use with Amber Eugene Yedvabny
Sunday, 15 December 2013
- Re: [AMBER] Proper Algorithm for GPU? case
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state Kamali Sripathi
- Re: [AMBER] MMPBSA.py strip_mask issue psu4.uic.edu
- [AMBER] Help: Producing a Prmtop file for a Truncated-Protein Trajectory #YIP YEW MUN#
Monday, 16 December 2013
- [AMBER] Manually extending the size of the virtual box Eugene Yedvabny
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state FyD
- Re: [AMBER] Manually extending the size of the virtual box David A Case
- Re: [AMBER] Help: Producing a Prmtop file for a Truncated-Protein Trajectory Jason Swails
- Re: [AMBER] MMPBSA.py strip_mask issue Jason Swails
- Re: [AMBER] Need some advice on calculating diffusion constant Brian Radak
- [AMBER] amber QM/MM :vlimit exceeded for step 1; vmax = 71.9072 Fengxue Li
- Re: [AMBER] amber QM/MM :vlimit exceeded for step 1; vmax = 71.9072 Brian Radak
- [AMBER] MMPBSA: eneopt=1 versus eneopt=3 Vlad Cojocaru
- Re: [AMBER] amber QM/MM :vlimit exceeded for step 1; vmax = 71.9072 Ross Walker
- Re: [AMBER] Manually extending the size of the virtual box Eugene Yedvabny
- Re: [AMBER] Manually extending the size of the virtual box Carlos Simmerling
- Re: [AMBER] Manually extending the size of the virtual box Jason Swails
- [AMBER] Improper terms in Amber Meng
- Re: [AMBER] MMPBSA errors :failed with prmtop Ray Luo, Ph.D.
- Re: [AMBER] Improper terms in Amber case
- Re: [AMBER] Manually extending the size of the virtual box Eugene Yedvabny
Tuesday, 17 December 2013
- [AMBER] MMPBSA of protein_DNA complex Aditya sarkar
- Re: [AMBER] MMPBSA of protein_DNA complex Vlad Cojocaru
- Re: [AMBER] The use of ansiotropic & semi-anisotropic pressure couplings in bilayer simulation. Dickson, Callum J
- [AMBER] CpptrajPairDist JAIME RUBIO MARTINEZ
- Re: [AMBER] CpptrajPairDist Daniel Roe
- Re: [AMBER] CpptrajPairDist Daniel Roe
- [AMBER] MMGBSA Entropy Error: Trajectory _MMPBSA_complex.mdcrd.1 has 0 frames! Cuiyl
- [AMBER] Is restart file size different between minimization and heating MD? Biao Ma
- [AMBER] Error while visualizing radius of gyration graph Sumra Wajid Abbasi 30-FBAS/MSBI/F09
Wednesday, 18 December 2013
- [AMBER] AMD simulation Mele N.
- Re: [AMBER] AMD simulation Mele N.
- Re: [AMBER] Is restart file size different between minimization and heating MD? David A Case
- Re: [AMBER] Error while visualizing radius of gyration graph David A Case
- Re: [AMBER] Error while visualizing radius of gyration graph Jonathan Sheehan
Thursday, 19 December 2013
- [AMBER] Bad atom type error during MMGBSA decomposition calsulations 王衍
- [AMBER] How to decompose PMF into electrostatic and van der Waals contributions. zhongqiao hu
- [AMBER] MMPBSA with inp=1 Vlad Cojocaru
- [AMBER] Regarding distance between residue masks (ptraj) agarai.physics.iisc.ernet.in
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions. Brian Radak
- Re: [AMBER] Regarding distance between residue masks (ptraj) Daniel Roe
- Re: [AMBER] Regarding distance between residue masks (ptraj) Jason Swails
- Re: [AMBER] Bad atom type error during MMGBSA decomposition calsulations Jason Swails
- Re: [AMBER] Is restart file size different between minimization and heating MD? Biao Ma
- Re: [AMBER] MMPBSA with inp=1 Ray Luo, Ph.D.
- Re: [AMBER] MMPBSA with inp=1 Vlad Cojocaru
- Re: [AMBER] MMPBSA with inp=1 Ray Luo, Ph.D.
- Re: [AMBER] MMPBSA with inp=1 wmsmith.uci.edu
- Re: [AMBER] MMPBSA with inp=1 wmsmith.uci.edu
- [AMBER] status of the Amber lipid framework? Sally Pias
- Re: [AMBER] status of the Amber lipid framework? Ross Walker
- Re: [AMBER] Puzzles about calculating binding energy using MMGBSA Jason Swails
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions zhongqiao hu
- [AMBER] RE： Bad atom type error during MMGBSA decompositioncalsulations wangyanforward.gmail.com
- [AMBER] RMSD-based clustering in CPPTRAJ/PTRAJ anu chandra
- [AMBER] FINAL_RESULTS_MMPBSA error filip fratev
- [AMBER] Problems of invoking the Amber 12 Yanyan ZHU
Friday, 20 December 2013
- Re: [AMBER] capturing free energy landscape anu chandra
- Re: [AMBER] FINAL_RESULTS_MMPBSA error Jason Swails
- Re: [AMBER] Problems of invoking the Amber 12 Jason Swails
- Re: [AMBER] capturing free energy landscape Jason Swails
- Re: [AMBER] capturing free energy landscape Thomas Evangelidis
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions David A Case
- Re: [AMBER] RMSD-based clustering in CPPTRAJ/PTRAJ Daniel Roe
- [AMBER] ANTECHAMBER PROBLEM Arjun Sharma
- [AMBER] cpptraj can not pass empty trajectory entry which is ok for ptraj Asaminew Haile
- Re: [AMBER] cpptraj can not pass empty trajectory entry which is ok for ptraj ros
- Re: [AMBER] cpptraj can not pass empty trajectory entry which is ok for ptraj Daniel Roe
- Re: [AMBER] cpptraj can not pass empty trajectory entry which is ok for ptraj Asaminew Haile
- Re: [AMBER] ANTECHAMBER PROBLEM David A Case
Saturday, 21 December 2013
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions zhongqiao hu
- [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure filip fratev
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Ross Walker
- [AMBER] Problems of invoking the Amber 12 and calculating the energy of each residue using the MMPBSA Yanyan ZHU
Sunday, 22 December 2013
- Re: [AMBER] Regarding distance between residue masks (ptraj) agarai.physics.iisc.ernet.in
Monday, 23 December 2013
- [AMBER] doubt in alanine scanning of phosphorylated residue suma jayakrishnan
- [AMBER] MMPBSA for single re-minimised coordinate sunita gupta
- Re: [AMBER] doubt in alanine scanning of phosphorylated residue Jason Swails
- Re: [AMBER] MMPBSA for single re-minimised coordinate Jason Swails
- Re: [AMBER] MMPBSA with inp=1 Ray Luo, Ph.D.
- [AMBER] ErrorWithLeap JAIME RUBIO MARTINEZ
- Re: [AMBER] ErrorWithLeap case
- Re: [AMBER] ErrorWithLeap case
- Re: [AMBER] ErrorWithLeap Jason Swails
- [AMBER] amber parameter for S2P (phosphoserine) sunita.tifrh.res.in
Tuesday, 24 December 2013
- Re: [AMBER] amber parameter for S2P (phosphoserine) sunita.tifrh.res.in
- [AMBER] problems in nmode and -use-mdins option (MMPBSA.py) houcemeddine
- Re: [AMBER] ErrorWithLeap JAIME RUBIO MARTINEZ
- Re: [AMBER] ErrorWithLeap Jason Swails
- Re: [AMBER] problems in nmode and -use-mdins option (MMPBSA.py) Jason Swails
- Re: [AMBER] doubt in alanine scanning of phosphorylated residue Jason Swails
- Re: [AMBER] problems in nmode and -use-mdins option (MMPBSA.py) houcemeddine
- Re: [AMBER] amber parameter for S2P (phosphoserine) Jonathan Sheehan
- [AMBER] Polarizing solute in non-polarizing solvent Hemant Gangwar
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions Brian Radak
- [AMBER] Fwd: doubt in alanine scanning of phosphorylated residue suma jayakrishnan
- [AMBER] Simulating protein with Fe atom onetwo
Wednesday, 25 December 2013
- [AMBER] input file with leap or antechamber? Zahra Khatti
- Re: [AMBER] input file with leap or antechamber? Ye MEI
- [AMBER] Errors about the values of PBSUR when calculating binding energy using MMPBSA Yanyan ZHU
- [AMBER] Fwd: Asfa Ali
- [AMBER] Amber Asfa Ali
- Re: [AMBER] Errors about the values of PBSUR when calculating binding energy using MMPBSA Jason Swails
- [AMBER] modified the amber parameter Saeed Nasiri
- Re: [AMBER] Fwd: Jason Swails
- Re: [AMBER] modified the amber parameter Jason Swails
- [AMBER] unable to recognize Chlorine atom even after defining in lib and frcmod file onetwo
Thursday, 26 December 2013
- [AMBER] cpptraj clustering Neha Gandhi
- Re: [AMBER] capturing free energy landscape anu chandra
- Re: [AMBER] Fwd: Asfa Ali
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions zhongqiao hu
- Re: [AMBER] capturing free energy landscape Daniel Roe
- Re: [AMBER] cpptraj clustering Daniel Roe
- Re: [AMBER] unable to recognize Chlorine atom even after defining in lib and frcmod file case
- Re: [AMBER] Simulating protein with Fe atom case
- Re: [AMBER] Polarizing solute in non-polarizing solvent case
- Re: [AMBER] Manually extending the size of the virtual box case
- [AMBER] RMSD vs RMSF vs nofit-RMSD Nitin Sharma
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions Jason Swails
- [AMBER] Problems about invoking AMBER12 in calculating binding energy Yanyan ZHU
- Re: [AMBER] Fwd: Jason Swails
- Re: [AMBER] Problems about invoking AMBER12 in calculating binding energy Jason Swails
- Re: [AMBER] unable to recognize Chlorine atom even after defining in lib and frcmod file onetwo
- [AMBER] Problem when calculating MMPBSA dongying0512
- [AMBER] Problem when calculating MMPBSA dongying0512
- Re: [AMBER] Problem when calculating MMPBSA Jason Swails
Friday, 27 December 2013
- Re: [AMBER] RMSD vs RMSF vs nofit-RMSD vadiraj kurdekar
- [AMBER] xLeap Himanshu Joshi
- Re: [AMBER] RMSD vs RMSF vs nofit-RMSD Daniel Roe
- Re: [AMBER] unable to recognize Chlorine atom even after defining in lib and frcmod file case
- Re: [AMBER] xLeap case
- Re: [AMBER] RMSD vs RMSF vs nofit-RMSD Nitin Sharma
- [AMBER] binding free energy and pose analysis Nitin Sharma
- [AMBER] AMDTutorial Ibrahim Said
- Re: [AMBER] xLeap Jio M
- Re: [AMBER] xLeap Bill Ross
- Re: [AMBER] binding free energy and pose analysis case
Saturday, 28 December 2013
- Re: [AMBER] Fwd: Asfa Ali
- Re: [AMBER] binding free energy and pose analysis Nitin Sharma
- [AMBER] sander's Segmentation fault Saeed Nasiri
- Re: [AMBER] binding free energy and pose analysis case
- Re: [AMBER] sander's Segmentation fault case
- Re: [AMBER] Fwd: Jason Swails
- Re: [AMBER] CpptrajPairDist JAIME RUBIO MARTINEZ
- [AMBER] Finding difficulty during calculation of diffusion coefficient from MSD plot Sohag Biswas
Sunday, 29 December 2013
- Re: [AMBER] binding free energy and pose analysis Nitin Sharma
- Re: [AMBER] binding free energy and pose analysis Jason Swails
- Re: [AMBER] binding free energy and pose analysis Nitin Sharma
- Re: [AMBER] Problem when calculating MMPBSA (Jason Swails) dongying0512
- [AMBER] request for help in water shell and closest command Robin Jain
Monday, 30 December 2013
- [AMBER] Tleap Problem - Unable to bond atoms in amide linkages #YIP YEW MUN#
- Re: [AMBER] Tleap Problem - Unable to bond atoms in amide linkages Mohammed Khaled Tumbi
- Re: [AMBER] Tleap Problem - Unable to bond atoms in amide linkages Yip Yew Mun
- Re: [AMBER] capturing free energy landscape anu chandra
- Re: [AMBER] Tleap Problem - Unable to bond atoms in amide linkages David A Case
- [AMBER] angle restraint with atom groups Sourav Purohit
- Re: [AMBER] angle restraint with atom groups David A Case
- [AMBER] SQM seems to run out of memory? Jonathan Saboury
- [AMBER] how to minimize with full electrostatics and no boundary conditions? Jose Borreguero
- Re: [AMBER] how to minimize with full electrostatics and no boundary conditions? Jason Swails
- Re: [AMBER] how to minimize with full electrostatics and no boundary conditions? Jose Borreguero
- Re: [AMBER] angle restraint with atom groups Sourav Purohit
- [AMBER] AMBER Asfa Ali
- Re: [AMBER] Fwd: Asfa Ali
Tuesday, 31 December 2013
- Re: [AMBER] SQM seems to run out of memory? David A Case
- Re: [AMBER] how to minimize with full electrostatics and no boundary conditions? David A Case
- Re: [AMBER] AMBER Daniel Roe
- Re: [AMBER] capturing free energy landscape Daniel Roe
- Re: [AMBER] request for help in water shell and closest command Daniel Roe
- Re: [AMBER] RMSD vs RMSF vs nofit-RMSD Daniel Roe
- [AMBER] C12 from OL Rejwan
- Re: [AMBER] how to minimize with full electrostatics and no boundary conditions? Jose Borreguero

Last message date: Tue Dec 31 2013 - 11:30:02 PST
Archived on: Fri Apr 26 2024 - 05:54:56 PDT

Amber Archive Dec 2013 by date