Amber Archive Jun 2012: by date

Thursday, 31 May 2012
- [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Cao Yang
- Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Cao Yang
- Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Cao Yang
- Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Cao Yang
- [AMBER] cuda errors Jonathan Gough
- [AMBER] ptraj Hbond analysis shradhey gupta
- [AMBER] ptraj Hbond analysis shradhey gupta
- Re: [AMBER] problem with solute that breaks up gaoya
Friday, 1 June 2012
- [AMBER] MMPBSA_Error: Could not find necessary program [sander] Cao Yang
- Re: [AMBER] Trouble calculating free energy steinbrt.rci.rutgers.edu
- [AMBER] chloride ions outside the box Francesco Pietra
- Re: [AMBER] Amber 12 on x86_64 CentOS 5 - SOLVED Kevin Parkes
- [AMBER] Effect of Temperature Soumya Lipsa Rath
- Re: [AMBER] MMPBSA_Error: Could not find necessary program [sander] Jason Swails
- Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Jason Swails
- Re: [AMBER] Effect of Temperature Jason Swails
- [AMBER] Fwd: problem with running equilibration MD in an LES system Sajeewa Pemasinghe
- Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Cao Yang
- Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Jason Swails
- Re: [AMBER] MMPBSA_Error: Could not find necessary program [sander] Cao Yang
- Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Cao Yang
- Re: [AMBER] Fwd: problem with running equilibration MD in an LES system David A Case
- Re: [AMBER] am1d problem Gabriel Jara
- Re: [AMBER] Fwd: problem with running equilibration MD in an LES system Sajeewa Pemasinghe
- Re: [AMBER] MMPBSA_Error: Could not find necessary program [sander] Bill Miller III
- Re: [AMBER] cuda errors Jonathan Gough
- Re: [AMBER] Fwd: problem with running equilibration MD in an LES system David A Case
- [AMBER] cuda parallel - can't find mpi.h Jonathan Gough
- Re: [AMBER] cuda parallel - can't find mpi.h Jason Swails
- [AMBER] Configurational bias Monte Carlo Benjamin Haley
- Re: [AMBER] cuda parallel - can't find mpi.h Ross Walker
- Re: [AMBER] cuda parallel - can't find mpi.h Jonathan Gough
- Re: [AMBER] cuda parallel - can't find mpi.h David A Case
- Re: [AMBER] Configurational bias Monte Carlo David A Case
- [AMBER] No C-terminal GLH in aminoct*.in Marc van der Kamp
- Re: [AMBER] Configurational bias Monte Carlo Jason Swails
- Re: [AMBER] No C-terminal GLH in aminoct*.in Jason Swails
- [AMBER] is there a batch queue app? Jonathan Gough
- Re: [AMBER] is there a batch queue app? Scott Le Grand
- Re: [AMBER] is there a batch queue app? Jason Swails
- Re: [AMBER] is there a batch queue app? Anselm Horn
- [AMBER] rocks cluster: MD is much slower when using more than one node Junmei Wang
- Re: [AMBER] is there a batch queue app? Jonathan Gough
- Re: [AMBER] Fwd: problem with running equilibration MD in an LES system Brian Radak
- Re: [AMBER] Fwd: problem with running equilibration MD in an LES system Sajeewa Pemasinghe
- Re: [AMBER] Effect of Temperature Soumya Lipsa Rath
- Re: [AMBER] Effect of Temperature Hai Nguyen
- Re: [AMBER] Effect of Temperature Soumya Lipsa Rath
- [AMBER] decomposition of potential of mean force into free energy contribution caobb0214
- Re: [AMBER] Trouble calculating free energy Aldo Segura
- [AMBER] ptraj Hbond analysis shradhey gupta
Saturday, 2 June 2012
- Re: [AMBER] rocks cluster: MD is much slower when using more than one node Dmitry Mukha
- Re: [AMBER] rocks cluster: MD is much slower when using more than one node case
- [AMBER] Trouble calculating free energy bmartini
- Re: [AMBER] rocks cluster: MD is much slower when using more than one node Junmei Wang
- Re: [AMBER] No C-terminal GLH in aminoct*.in FyD
Sunday, 3 June 2012
- Re: [AMBER] rocks cluster: MD is much slower when using more than one node Matthew Zwier
- [AMBER] inpcrd Dr. Vitaly V. Chaban
- Re: [AMBER] inpcrd Daniel Roe
- Re: [AMBER] inpcrd Dr. Vitaly V. Chaban
- [AMBER] how to change the namme of the terminal OXT so that it can be recoginized by MOLMOL Acoot Brett
Monday, 4 June 2012
- Re: [AMBER] how to change the namme of the terminal OXT so that it can be recoginized by MOLMOL steinbrt.rci.rutgers.edu
- [AMBER] Distance constraints not working.. Kumar, Sonu
- [AMBER] Problem in parameter file generation Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] Problem in parameter file generation Alex Rodriguez
- Re: [AMBER] Problem in parameter file generation Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] Problem in parameter file generation Alex Rodriguez
- Re: [AMBER] Problem in parameter file generation Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] Problem in parameter file generation Alex Rodriguez
- Re: [AMBER] Problem in parameter file generation Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] how to change the namme of the terminal OXT so that it can be recoginized by MOLMOL David A Case
- Re: [AMBER] Distance constraints not working.. David A Case
- [AMBER] Reallocation of memory space Debolina Mitra
- [AMBER] Antechamber problem monica.imtech.res.in
- [AMBER] Fwd: Fwd: problem with running equilibration MD in an LES system Sajeewa Pemasinghe
- Re: [AMBER] Fwd: Fwd: problem with running equilibration MD in an LES system Carlos Simmerling
- Re: [AMBER] Antechamber problem David A Case
- Re: [AMBER] Distance constraints not working.. Kumar, Sonu
- Re: [AMBER] Distance constraints not working.. Adrian Roitberg
- Re: [AMBER] Fwd: Fwd: problem with running equilibration MD in an LES system Sajeewa Pemasinghe
- [AMBER] compiling parallel on centOS5 - rocks with intel Jonathan Gough
- Re: [AMBER] compiling parallel on centOS5 - rocks with intel David A Case
- Re: [AMBER] ptraj Hbond analysis Thomas Cheatham
- Re: [AMBER] compiling parallel on centOS5 - rocks with intel Jonathan Gough
- Re: [AMBER] compiling parallel on centOS5 - rocks with intel Jason Swails
- Re: [AMBER] compiling parallel on centOS5 - rocks with intel Jonathan Gough
- Re: [AMBER] compiling parallel on centOS5 - rocks with intel Jason Swails
- Re: [AMBER] compiling parallel on centOS5 - rocks with intel Jonathan Gough
- Re: [AMBER] compiling parallel on centOS5 - rocks with intel Jason Swails
- [AMBER] nvidia GTX 550 Ti Michael Mayo
- [AMBER] Small molecule simulations Chris Chris
- Re: [AMBER] Small molecule simulations Dr. Vitaly V. Chaban
- Re: [AMBER] Small molecule simulations bmartini
- [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09
Tuesday, 5 June 2012
- Re: [AMBER] Error in minimization Ben Roberts
- Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09
- [AMBER] Amber11 Installation Problem arun kumar
- Re: [AMBER] Amber11 Installation Problem Rajeswari A.
- Re: [AMBER] Amber11 Installation Problem Daniel Roe
- Re: [AMBER] Error in minimization Daniel Roe
- Re: [AMBER] Amber11 Installation Problem Jason Swails
- Re: [AMBER] nvidia GTX 550 Ti Scott Le Grand
- Re: [AMBER] No C-terminal GLH in aminoct*.in Marc van der Kamp
- Re: [AMBER] No C-terminal GLH in aminoct*.in Jason Swails
- [AMBER] Problem with NAB: "Residue g not in library rna.amber94.rlb." Romelia Salomon
- Re: [AMBER] Problem with NAB: "Residue g not in library rna.amber94.rlb." David A. Case
- Re: [AMBER] Problem with NAB: "Residue g not in library rna.amber94.rlb." Romelia Salomon
- Re: [AMBER] Problem with NAB: "Residue g not in library rna.amber94.rlb." cieplak.cgl.ucsf.edu
- Re: [AMBER] is there a batch queue app? Jonathan Gough
- Re: [AMBER] Problem with NAB: "Residue g not in library rna.amber94.rlb." Romelia Salomon
- [AMBER] DMSO parameters Yun Shi
- Re: [AMBER] DMSO parameters Dr. Vitaly V. Chaban
- Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] No C-terminal GLH in aminoct*.in FyD
- [AMBER] Amber11 Installation Problem arun kumar
Wednesday, 6 June 2012
- Re: [AMBER] No C-terminal GLH in aminoct*.in Marc van der Kamp
- Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09
- [AMBER] MMPBSA.py - problem with complex.prmtop colvin
- [AMBER] Error in new installation. Catein Catherine
- Re: [AMBER] No C-terminal GLH in aminoct*.in FyD
- Re: [AMBER] Amber11 Installation Problem Jason Swails
- [AMBER] center of mass. Subrata Paul
- Re: [AMBER] MMPBSA.py - problem with complex.prmtop Bill Miller III
- Re: [AMBER] Amber11 Installation Problem arun kumar
- Re: [AMBER] Amber11 Installation Problem Jason Swails
- Re: [AMBER] Error in new installation. Jason Swails
- Re: [AMBER] Error in minimization Jason Swails
- [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11 Damodaran, Komath
- Re: [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11 Bill Miller III
- [AMBER] Convergence problems with rism1d and water model other than SPC Fabrício Bracht
- [AMBER] Convergence problems with rism1d and water model other than SPC Fabrício Bracht
- Re: [AMBER] Convergence problems with rism1d and water model other than SPC tluchko
- [AMBER] Why calcualted energy difference betwwen MM-PBSA and MM-GBSA is so large Delwar Hossain
- [AMBER] restraining residues with a gpu cluster Tom Patapoff
- [AMBER] Removing finite number of solvent particles from simulation box Adam Jion
- Re: [AMBER] restraining residues with a gpu cluster case
- Re: [AMBER] Removing finite number of solvent particles from simulation box Jason Swails
- Re: [AMBER] Removing finite number of solvent particles from simulation box Jason Swails
- Re: [AMBER] MMPBSA.py - problem with complex.prmtop colvin
- Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] Removing finite number of solvent particles from simulation box Adam Jion
Thursday, 7 June 2012
- [AMBER] Problems installing AmberTools12 on Ubuntu Adam Jion
- [AMBER] ptraj behaves differently on Mac and Linux Benjamin Stauch
- Re: [AMBER] Error in minimization David A Case
- Re: [AMBER] ptraj behaves differently on Mac and Linux Daniel Roe
- Re: [AMBER] Removing finite number of solvent particles from simulation box Jason Swails
- Re: [AMBER] Problems installing AmberTools12 on Ubuntu Jason Swails
- Re: [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11 Damodaran, Komath
- Re: [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11 Ray Luo, Ph.D.
- [AMBER] up coming workshop? Albert
- [AMBER] what version of xcode are you using? Jonathan Gough
- [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl Nan Li
- Re: [AMBER] what version of xcode are you using? Jason Swails
- Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl Jason Swails
- Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl Nan Li
- Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl Jason Swails
- Re: [AMBER] up coming workshop? Ross Walker
- [AMBER] FactorIX test: CUDA + MPI + ntt=2 => never ends Gerald Monard
- Re: [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11 Ray Luo, Ph.D.
- Re: [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11 Ray Luo, Ph.D.
- Re: [AMBER] Problems installing AmberTools12 on Ubuntu Adam Jion
- Re: [AMBER] Problems installing AmberTools12 on Ubuntu Jason Swails
- Re: [AMBER] Problems installing AmberTools12 on Ubuntu Adam Jion
- [AMBER] GBSA for simulation of disordered proteins Bashford, Donald
- Re: [AMBER] Problems installing AmberTools12 on Ubuntu Jason Swails
- Re: [AMBER] Problems installing AmberTools12 on Ubuntu Adam Jion
- [AMBER] unfolding with iwrap=1, 500K heating is enough? Chinh Su Tran To
- [AMBER] REMD equilibration Soumya Lipsa Rath
- Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09
- [AMBER] Generation of ESP files Debolina Mitra
Friday, 8 June 2012
- Re: [AMBER] up coming workshop? Albert
- Re: [AMBER] Generation of ESP files intra\\sa175950
- Re: [AMBER] up coming workshop? Albert
- Re: [AMBER] unfolding with iwrap=1, 500K heating is enough? Carlos Simmerling
- Re: [AMBER] REMD equilibration Carlos Simmerling
- Re: [AMBER] Problems installing AmberTools12 on Ubuntu Jason Swails
- Re: [AMBER] Error in minimization Jason Swails
- [AMBER] partial charge, charge radius and epsilon Acoot Brett
- Re: [AMBER] what version of xcode are you using? Jonathan Gough
- Re: [AMBER] what version of xcode are you using? Jason Swails
- Re: [AMBER] what version of xcode are you using? Jonathan Gough
- Re: [AMBER] Error in minimization David A Case
- [AMBER] FIX for Mac OS X Lion with Xcode 4.3.2 Jason Swails
- [AMBER] Problems matching atom names to PREP files Chris Whittleston
- Re: [AMBER] what version of xcode are you using? Jonathan Gough
- Re: [AMBER] Problems matching atom names to PREP files Daniel Roe
- Re: [AMBER] what version of xcode are you using? Jason Swails
- Re: [AMBER] partial charge, charge radius and epsilon Jason Swails
- Re: [AMBER] what version of xcode are you using? Jonathan Gough
- Re: [AMBER] Problems matching atom names to PREP files FyD
- Re: [AMBER] FIX for Mac OS X Lion with Xcode 4.3.2 David A Case
- Re: [AMBER] FIX for Mac OS X Lion with Xcode 4.3.2 Jason Swails
- Re: [AMBER] what version of xcode are you using? Jason Swails
- Re: [AMBER] what version of xcode are you using? Jonathan Gough
- Re: [AMBER] what version of xcode are you using? Jason Swails
- Re: [AMBER] what version of xcode are you using? Jonathan Gough
- Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl Nan Li
- Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl Jason Swails
- Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl Nan Li
- Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] FIX for Mac OS X Lion with Xcode 4.3.2 Jonathan Gough
- Re: [AMBER] FIX for Mac OS X Lion with Xcode 4.3.2 David A Case
- Re: [AMBER] Problems matching atom names to PREP files Bill Ross
- Re: [AMBER] REMD equilibration Soumya Lipsa Rath
Saturday, 9 June 2012
- Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl Nadine.Homeyer.uni-duesseldorf.de
- [AMBER] LEaP misplaces ions Francesco Pietra
- [AMBER] Fwd: LEaP misplaces ions Francesco Pietra
- Re: [AMBER] REMD equilibration Daniel Sindhikara
- Re: [AMBER] LEaP misplaces ions Bill Ross
- Re: [AMBER] LEaP misplaces ions Jason Swails
- Re: [AMBER] LEaP misplaces ions Francesco Pietra
- Re: [AMBER] LEaP misplaces ions Bill Ross
- [AMBER] Mac OS X Lion workaround Jason Swails
- Re: [AMBER] REMD equilibration Hai Nguyen
- Re: [AMBER] LEaP misplaces ions Francesco Pietra
Sunday, 10 June 2012
- Re: [AMBER] LEaP misplaces ions Robin Betz
- Re: [AMBER] LEaP misplaces ions Francesco Pietra
- Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] Error in minimization Daniel Sindhikara
- Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] REMD equilibration Soumya Lipsa Rath
- Re: [AMBER] Error in minimization Daniel Sindhikara
- Re: [AMBER] unfolding with iwrap=1, 500K heating is enough? Chinh Su Tran To
Monday, 11 June 2012
- [AMBER] protein misplaced into the water box Francesco Pietra
- [AMBER] MMPBSA calculation reproducibility Sangita Kachhap
- [AMBER] Amber12 Compilation Error in CENTOS 4.5 BERGY
- [AMBER] How to get starting geometry for <10 AA peptides? Catein Catherine
- Re: [AMBER] Mac OS X Lion workaround Jason Swails
- Re: [AMBER] How to get starting geometry for <10 AA peptides? Jonathan Gough
- [AMBER] FF param William Henry BISSON
- Re: [AMBER] FF param Giulia
- [AMBER] FF12SB + GLYCAM_06h + Fluorine Kevin Parkes
- [AMBER] QM/MM minimization Ewa Chudyk
- Re: [AMBER] QM/MM minimization Adrian Roitberg
- Re: [AMBER] MMPBSA calculation reproducibility Ray Luo, Ph.D.
- Re: [AMBER] FF12SB + GLYCAM_06h + Fluorine Lachele Foley (Lists)
- [AMBER] Bug in resp or respgen? using intra-molecular-charge-constraints... Marko Wehle
- Re: [AMBER] MMPBSA calculation reproducibility Sangita Kachhap
- [AMBER] mmpbsa kirtana S
- Re: [AMBER] MMPBSA calculation reproducibility Ray Luo, Ph.D.
- [AMBER] QM/MM periodic boundary conditions in Amber Ivan Ufimtsev
- [AMBER] parameters and charges for R and S Configurations Jio M
- Re: [AMBER] protein misplaced into the water box Bill Ross
- [AMBER] Fw: parameters and charges for R and S Configurations Jio M
- Re: [AMBER] QM/MM periodic boundary conditions in Amber Ross Walker
- [AMBER] ptraj: combine pdb's to mdcrd Do-Yong Kim
- Re: [AMBER] Error in minimization Ben Roberts
- Re: [AMBER] QM/MM periodic boundary conditions in Amber case
- Re: [AMBER] mmpbsa case
- [AMBER] Abnormally Slow NMode entropy calculation Cao Yang
- Re: [AMBER] parameters and charges for R and S Configurations FyD
- Re: [AMBER] Bug in resp or respgen? using intra-molecular-charge-constraints... FyD
Tuesday, 12 June 2012
- Re: [AMBER] parameters and charges for R and S Configurations Jio M
- Re: [AMBER] protein misplaced into the water box Francesco Pietra
- Re: [AMBER] FF12SB + GLYCAM_06h + Fluorine Kevin Parkes
- Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09
- [AMBER] Value of internal dielectric constant ? for per residue decomposition free energy calculation using MMGBSA method Jignesh Patel
- Re: [AMBER] Abnormally Slow NMode entropy calculation Jason Swails
- Re: [AMBER] Value of internal dielectric constant ? for per residue decomposition free energy calculation using MMGBSA method Jason Swails
- [AMBER] diffusion coefficient Subrata Paul
- [AMBER] Amber cuda test failure jani vinod
- Re: [AMBER] FF12SB + GLYCAM_06h + Fluorine David A Case
- Re: [AMBER] mmpbsa kirtana S
- Re: [AMBER] Value of internal dielectric constant ? for per residue decomposition free energy calculation using MMGBSA method Jignesh Patel
- Re: [AMBER] mmpbsa David A Case
- Re: [AMBER] mmpbsa Jason Swails
- Re: [AMBER] Bug in resp or respgen? using intra-molecular-charge-constraints... Marko Wehle
- Re: [AMBER] protein misplaced into the water box Bill Ross
- Re: [AMBER] ptraj: combine pdb's to mdcrd Jason Swails
- [AMBER] The VDWAALS is huge in MMPBSA calculation. qiao xue
- Re: [AMBER] The VDWAALS is huge in MMPBSA calculation. Bill Miller III
- [AMBER] what is vlimit error? Sanjib Paul
- [AMBER] where is velocity information? Albert
- Re: [AMBER] The VDWAALS is huge in MMPBSA calculation. qiao xue
- [AMBER] how to assign bond order for the output of RED .mol2? Albert
Wednesday, 13 June 2012
- Re: [AMBER] Bug in resp or respgen? using intra-molecular-charge-constraints... FyD
- Re: [AMBER] what is vlimit error? Scott Brozell
- Re: [AMBER] how to assign bond order for the output of RED .mol2? FyD
- Re: [AMBER] how to assign bond order for the output of RED .mol2? FyD
- [AMBER] A small point of confusion in 3DRISM outfiles Daniel Sindhikara
- Re: [AMBER] The VDWAALS is huge in MMPBSA calculation. Bill Miller III
- Re: [AMBER] what is vlimit error? David A Case
- Re: [AMBER] A small point of confusion in 3DRISM outfiles Tyler Luchko
- Re: [AMBER] where is velocity information? Brian Radak
- [AMBER] calculation the entropy of a membrane DPPC-protein-ligand complex xiaojiong
- [AMBER] unit of energy Nan Li
- Re: [AMBER] mmpbsa kirtana S
- [AMBER] ptraj cannot handle large crd file vishal kumar Jaiswal
- Re: [AMBER] ptraj cannot handle large crd file vishal kumar Jaiswal
- Re: [AMBER] ptraj cannot handle large crd file Daniel Roe
- Re: [AMBER] The VDWAALS is huge in MMPBSA calculation. Cao Yang
Thursday, 14 June 2012
- Re: [AMBER] what is vlimit error? Scott Brozell
- [AMBER] Regarding running PME simulation on GPU jani vinod
- Re: [AMBER] Regarding running PME simulation on GPU Ross Walker
- Re: [AMBER] mmpbsa David A Case
- [AMBER] whether it is proper to strip DPPCs xiaojiong
- [AMBER] strange POPC under lipids 11 FF Albert
- Re: [AMBER] strange POPC under lipids 11 FF Ross Walker
- [AMBER] acpye for CHARMM? Albert
- [AMBER] Leap. Error messages on renaming ASP to AS4 etc. George Tzotzos
- Re: [AMBER] unfolding with iwrap=1, 500K heating is enough? Carlos Simmerling
- Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. Dwight McGee
- [AMBER] Help with Zn parameters after MCPB parameterization Fabrício Bracht
- Re: [AMBER] REMD equilibration Carlos Simmerling
- [AMBER] force field library for protonated cytosine Asmita Gupta
- Re: [AMBER] force field library for protonated cytosine Jason Swails
- Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. George Tzotzos
- Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. Marc van der Kamp
- Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. Jason Swails
- Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. George Tzotzos
- Re: [AMBER] force field library for protonated cytosine David A Case
- Re: [AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues sudipta
- Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. David A Case
- Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. Marc van der Kamp
- Re: [AMBER] Help with Zn parameters after MCPB parameterization Ben Roberts
- Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. Jason Swails
- Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. George Tzotzos
- Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. Jason Swails
- [AMBER] Facing problem on TUTORIAL A1 sudipta
- [AMBER] undefined reference error in compiling Xin Geng
- Re: [AMBER] undefined reference error in compiling Ben Roberts
- Re: [AMBER] undefined reference error in compiling Jason Swails
- Re: [AMBER] undefined reference error in compiling case
- Re: [AMBER] REMD equilibration Daniel Sindhikara
- Re: [AMBER] REMD equilibration Soumya Lipsa Rath
- [AMBER] long range LJ correction; surface tension; trajectory MD
Friday, 15 June 2012
- Re: [AMBER] Facing problem on TUTORIAL A1 steinbrt.rci.rutgers.edu
- [AMBER] R: strange POPC under lipids 11 FF Giovanni Pavan
- Re: [AMBER] REMD equilibration Daniel Sindhikara
- Re: [AMBER] R: strange POPC under lipids 11 FF Ross Walker
- Re: [AMBER] R: strange POPC under lipids 11 FF Albert
- [AMBER] GPU kernel error Fernando Martín García
- Re: [AMBER] R: strange POPC under lipids 11 FF Ross Walker
- Re: [AMBER] R: strange POPC under lipids 11 FF Albert
- Re: [AMBER] REMD equilibration Carlos Simmerling
- Re: [AMBER] R: strange POPC under lipids 11 FF Ross Walker
- Re: [AMBER] long range LJ correction; surface tension; trajectory Carlos Simmerling
- [AMBER] Error with box parameters Карлов Дмитрий
- Re: [AMBER] R: strange POPC under lipids 11 FF Albert
- Re: [AMBER] acpye for CHARMM? Alan
- Re: [AMBER] The VDWAALS is huge in MMPBSA calculation. qiao xue
- [AMBER] Fail to read hem parameters written by P. Rydberg 崔颖璐
- Re: [AMBER] The VDWAALS is huge in MMPBSA calculation. Bill Miller III
- Re: [AMBER] Error with box parameters David A Case
- Re: [AMBER] GPU kernel error Scott Le Grand
- [AMBER] why cut off is so small for CUDA running? Albert
- Re: [AMBER] The VDWAALS is huge in MMPBSA calculation. qiao xue
- Re: [AMBER] GPU kernel error Fernando Martín García
- Re: [AMBER] Fail to read hem parameters written by P. Rydberg Mark Williamson
- Re: [AMBER] The VDWAALS is huge in MMPBSA calculation. Jason Swails
- Re: [AMBER] why cut off is so small for CUDA running? Daniel Roe
- Re: [AMBER] REMD equilibration Jason Swails
- Re: [AMBER] REMD equilibration Daniel Roe
- [AMBER] R: R: strange POPC under lipids 11 FF Giovanni Pavan
- Re: [AMBER] R: strange POPC under lipids 11 FF Adrian Roitberg
- Re: [AMBER] R: R: strange POPC under lipids 11 FF Marek Maly
- Re: [AMBER] REMD equilibration Soumya Lipsa Rath
- Re: [AMBER] REMD equilibration Carlos Simmerling
- Re: [AMBER] undefined reference error in compiling Xin Geng
- Re: [AMBER] undefined reference error in compiling Jason Swails
- Re: [AMBER] R: strange POPC under lipids 11 FF Albert
- Re: [AMBER] force field library for protonated cytosine FyD
- Re: [AMBER] Facing problem on TUTORIAL A1 sudipta
- [AMBER] chiral Sulfur atom Yun Shi
- Re: [AMBER] GPU kernel error Ross Walker
- Re: [AMBER] R: strange POPC under lipids 11 FF Ross Walker
- Re: [AMBER] R: R: strange POPC under lipids 11 FF Ross Walker
- Re: [AMBER] R: strange POPC under lipids 11 FF Ross Walker
- [AMBER] MMPBSA.py Delwar Hossain
- Re: [AMBER] MMPBSA.py manikanthan bhavaraju
- [AMBER] umbrella sampling -- centroid or center of mass Junjian Miao
- Re: [AMBER] umbrella sampling -- centroid or center of mass David A. Case
- Re: [AMBER] undefined reference error in compiling David A. Case
- Re: [AMBER] undefined reference error in compiling Jason Swails
- Re: [AMBER] MMPBSA.py Jason Swails
- Re: [AMBER] REMD equilibration Soumya Lipsa Rath
- [AMBER] Job running problem in sander Souvik Sur
- Re: [AMBER] chiral Sulfur atom FyD
Saturday, 16 June 2012
- Re: [AMBER] R: strange POPC under lipids 11 FF Vlad Cojocaru
- Re: [AMBER] R: R: strange POPC under lipids 11 FF Marek Maly
- [AMBER] Cuda performance HIMANSHU JOSHI
- Re: [AMBER] REMD equilibration Carlos Simmerling
- Re: [AMBER] Job running problem in sander Daniel Roe
- Re: [AMBER] REMD equilibration Soumya Lipsa Rath
- Re: [AMBER] R: strange POPC under lipids 11 FF David A. Case
- Re: [AMBER] R: strange POPC under lipids 11 FF Ross Walker
- Re: [AMBER] Cuda performance Ross Walker
- Re: [AMBER] R: strange POPC under lipids 11 FF Ross Walker
- Re: [AMBER] R: strange POPC under lipids 11 FF Vlad Cojocaru
- Re: [AMBER] R: R: strange POPC under lipids 11 FF Benjamin D Madej
- Re: [AMBER] R: strange POPC under lipids 11 FF Albert
- Re: [AMBER] R: strange POPC under lipids 11 FF Vlad Cojocaru
- Re: [AMBER] R: strange POPC under lipids 11 FF Benjamin D Madej
- Re: [AMBER] R: strange POPC under lipids 11 FF Tales Yuan
- Re: [AMBER] R: strange POPC under lipids 11 FF Tales Yuan
- Re: [AMBER] R: strange POPC under lipids 11 FF Benjamin D Madej
- Re: [AMBER] R: strange POPC under lipids 11 FF Albert
- [AMBER] duplicating - multiplying input files to create dimer etc. Jonathan Gough
- Re: [AMBER] duplicating - multiplying input files to create dimer etc. Jason Swails
- Re: [AMBER] duplicating - multiplying input files to create dimer etc. Jonathan Gough
- [AMBER] MMPBSA.py.MPI Delwar Hossain
- Re: [AMBER] MMPBSA.py.MPI Bill Miller III
- [AMBER] Problem of Force filed (Calculate the dihedral parameter) Takeshi Baba
- Re: [AMBER] Problem of Force filed (Calculate the dihedral parameter) Adrian Roitberg
Sunday, 17 June 2012
- Re: [AMBER] Cuda performance HIMANSHU JOSHI
- Re: [AMBER] GPU kernel error Dmitry Mukha
- Re: [AMBER] Facing problem on TUTORIAL A1 steinbrt.rci.rutgers.edu
- Re: [AMBER] GPU kernel error Ross Walker
- Re: [AMBER] GPU kernel error Dmitry Mukha
- [AMBER] C- and N-terminal amino acids in AmberTools 1.4 Kamali Sripathi
- Re: [AMBER] C- and N-terminal amino acids in AmberTools 1.4 Jason Swails
- [AMBER] Ion clumping in large protein-RNA systems Kamali Sripathi
- Re: [AMBER] C- and N-terminal amino acids in AmberTools 1.4 Kamali Sripathi
- Re: [AMBER] why cut off is so small for CUDA running? Scott Le Grand
- Re: [AMBER] Ion clumping in large protein-RNA systems Daniel Sindhikara
- Re: [AMBER] Regarding running PME simulation on GPU jani vinod
- Re: [AMBER] unfolding with iwrap=1, 500K heating is enough? Chinh Su Tran To
- Re: [AMBER] why cut off is so small for CUDA running? Ross Walker
- [AMBER] How to calculate distance between Center of Axis (DNA) to Center of Mass of Ligand in ptraj Muhammad Khaled Tumbi
Monday, 18 June 2012
- Re: [AMBER] long range LJ correction; surface tension; trajectory MD
- [AMBER] Atom type for oxygen bound to Phosphate Dilraj LAMA
- Re: [AMBER] Atom type for oxygen bound to Phosphate David A. Case
- Re: [AMBER] Ion clumping in large protein-RNA systems Kamali Sripathi
- Re: [AMBER] Atom type for oxygen bound to Phosphate FyD
- Re: [AMBER] Fail to read hem parameters written by P. Rydberg 崔颖璐
- Re: [AMBER] unfolding with iwrap=1, 500K heating is enough? Jason Swails
- Re: [AMBER] (no subject) DEBOSTUTI GHOSHDASTIDAR
- [AMBER] POPE lipids is too 'ordered' Albert
- Re: [AMBER] Atom type for oxygen bound to Phosphate FyD
- Re: [AMBER] POPE lipids is too 'ordered' Benjamin D Madej
- Re: [AMBER] (no subject) David A. Case
- Re: [AMBER] POPE lipids is too 'ordered' Albert
- Re: [AMBER] POPE lipids is too 'ordered' Benjamin D Madej
- Re: [AMBER] POPE lipids is too 'ordered' Albert
- [AMBER] modeling GDP Brandon Sim
- [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht
- Re: [AMBER] undefined reference error in compiling Xin Geng
- Re: [AMBER] modeling GDP David A. Case
- Re: [AMBER] modeling GDP FyD
- Re: [AMBER] modeling GDP Brandon Sim
- [AMBER] Script error to restart MD automatically Tommy Yap
- Re: [AMBER] Script error to restart MD automatically Niel Henriksen
- Re: [AMBER] Script error to restart MD automatically Tommy Yap
- [AMBER] MMPBSA problem marawan hussain
- [AMBER] RESP charges for single nucleic acid residue Yun Shi
- Re: [AMBER] GPU kernel error Dmitry Mukha
Tuesday, 19 June 2012
- Re: [AMBER] Script error to restart MD automatically Anselm Horn
- Re: [AMBER] Script error to restart MD automatically Tommy Yap
- [AMBER] ptraj vector error Albert
- Re: [AMBER] ptraj vector error Marc van der Kamp
- Re: [AMBER] modeling GDP David A. Case
- Re: [AMBER] ptraj vector error Albert
- Re: [AMBER] ptraj vector error Marc van der Kamp
- [AMBER] Slow jobs Cao Yang
- Re: [AMBER] why cut off is so small for CUDA running? Martin Andersson
- Re: [AMBER] ptraj vector error Albert
- Re: [AMBER] POPE lipids is too 'ordered' Albert
- Re: [AMBER] POPE lipids is too 'ordered' Hannes Loeffler
- Re: [AMBER] POPE lipids is too 'ordered' Albert
- Re: [AMBER] POPE lipids is too 'ordered' Hannes Loeffler
- Re: [AMBER] Script error to restart MD automatically Adrian Roitberg
- [AMBER] Atom type for oxygen bound to Phosphate Dilraj LAMA
- Re: [AMBER] Ion clumping in large protein-RNA systems Thomas Cheatham
- [AMBER] Bad atom MN in free energy decomposition with MMPBSA.py Cao Yang
- Re: [AMBER] Ion clumping in large protein-RNA systems Kamali Sripathi
- Re: [AMBER] Ion clumping in large protein-RNA systems Robin Betz
- Re: [AMBER] Slow jobs Ross Walker
- Re: [AMBER] why cut off is so small for CUDA running? Ross Walker
- Re: [AMBER] GPU kernel error Ross Walker
- [AMBER] PB Bomb in epsmap(): epsy out of range Xiao Ba
- Re: [AMBER] PB Bomb in epsmap(): epsy out of range Ray Luo, Ph.D.
- [AMBER] problem with solvateShell command Sajeewa Pemasinghe
- Re: [AMBER] problem with solvateShell command Bill Ross
- Re: [AMBER] MMPBSA problem Bill Miller III
- Re: [AMBER] problem with solvateShell command Sajeewa Pemasinghe
- [AMBER] Sander output Error Souvik Sur
- Re: [AMBER] Sander output Error Jason Swails
- Re: [AMBER] modeling GDP Brandon Sim
- Re: [AMBER] GPU kernel error Adam Jion
- [AMBER] Switching-off the partial charges Adam Jion
- Re: [AMBER] Switching-off the partial charges Daniel Sindhikara
- Re: [AMBER] Switching-off the partial charges David A. Case
Wednesday, 20 June 2012
- Re: [AMBER] modeling GDP FyD
- Re: [AMBER] Switching-off the partial charges steinbrt.rci.rutgers.edu
- [AMBER] problem during heating up the system Sanjib Paul
- Re: [AMBER] problem during heating up the system chirag740.gmail.com
- Re: [AMBER] problem during heating up the system Sanjib Paul
- Re: [AMBER] problem during heating up the system David A. Case
- [AMBER] Constant pH simulation at pH 7 Nicholus Bhattacharjee
- Re: [AMBER] Constant pH simulation at pH 7 Jason Swails
- [AMBER] Entropy calculations with mm_pbsa.pl using amber12 manikanthan bhavaraju
- [AMBER] Problem while running MMPBSA qiqi
- Re: [AMBER] (no subject) DEBOSTUTI GHOSHDASTIDAR
- Re: [AMBER] Problem while running MMPBSA Jason Swails
- Re: [AMBER] Problem while running MMPBSA qiqi
- Re: [AMBER] Problem while running MMPBSA Jason Swails
- [AMBER] MMPBSA.py.MPI and MMPBSA.py Delwar Hossain
- [AMBER] Error in writing of coordinate file after simulation Ashutosh Shandilya
- Re: [AMBER] MMPBSA.py.MPI and MMPBSA.py Jason Swails
- [AMBER] rdf/count of ions around a protein E. Nihal Korkmaz
- Re: [AMBER] Problem with installing Amber 12 CUDA GPU version (NetCDF error) Ross Walker
- [AMBER] strange ion location Albert
Thursday, 21 June 2012
- [AMBER] Specifying disulfide bonds in a protein model Beale, John
- [AMBER] TI calculation Amber 12 Anna Bauß
- Re: [AMBER] Specifying disulfide bonds in a protein model Anselm Horn
- Re: [AMBER] TI calculation Amber 12 steinbrt.rci.rutgers.edu
- Re: [AMBER] TI calculation Amber 12 Anna Bauß
- Re: [AMBER] Specifying disulfide bonds in a protein model David A. Case
- Re: [AMBER] Error in writing of coordinate file after simulation Daniel Roe
- Re: [AMBER] TI calculation Amber 12 steinbrt.rci.rutgers.edu
- [AMBER] Solvent box specification for sander Brandon Sim
- Re: [AMBER] TI calculation Amber 12 Anna Bauß
- Re: [AMBER] Solvent box specification for sander Brian Radak
- [AMBER] strange ion location Albert
- Re: [AMBER] Solvent box specification for sander Jason Swails
- Re: [AMBER] TI calculation Amber 12 steinbrt.rci.rutgers.edu
- Re: [AMBER] Solvent box specification for sander Brandon Sim
- Re: [AMBER] Solvent box specification for sander Jason Swails
- Re: [AMBER] Solvent box specification for sander Brandon Sim
- Re: [AMBER] Solvent box specification for sander Jason Swails
- [AMBER] Issues with library location on compiling AmberTools12 Francesco Pietra
- [AMBER] R: strange POPC under lipids 11 FF J B
- [AMBER] idea of RMSD calculation in AMBER Sajeewa Pemasinghe
- Re: [AMBER] idea of RMSD calculation in AMBER Carlos Simmerling
- [AMBER] C-H...O hydrogen bonds? Schubert Mario
- Re: [AMBER] R: strange POPC under lipids 11 FF Albert
- Re: [AMBER] R: strange POPC under lipids 11 FF Vlad Cojocaru
- [AMBER] SOLVED Fwd: Issues with library location on compiling AmberTools12 Francesco Pietra
- Re: [AMBER] R: strange POPC under lipids 11 FF Albert
- Re: [AMBER] R: strange POPC under lipids 11 FF Vlad Cojocaru
- [AMBER] R: strange POPC under lipids 11 FF J B
- [AMBER] How to explain this phenomenon is production MD Acoot Brett
Friday, 22 June 2012
- Re: [AMBER] How to explain this phenomenon is production MD steinbrt.rci.rutgers.edu
- Re: [AMBER] Sander Error Melissa Buskes
- Re: [AMBER] R: strange POPC under lipids 11 FF Gould, Ian R
- Re: [AMBER] R: strange POPC under lipids 11 FF Albert
- Re: [AMBER] R: strange POPC under lipids 11 FF Vlad Cojocaru
- [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Elisa Frezza
- [AMBER] warning during nmode calulation - Not all of your snapshots minimized within tolerable limits for nmode Sangita Kachhap
- [AMBER] R: strange POPC under lipids 11 FF Joakim Jämbeck
- [AMBER] vacuum simulation fails using pmemd g t
- [AMBER] hydrogen bond analysis Urszula Uciechowska
- Re: [AMBER] R: strange POPC under lipids 11 FF Vlad Cojocaru
- Re: [AMBER] strange POPC under lipids 11 FF Vítor Félix
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Daniel Roe
- Re: [AMBER] C-H...O hydrogen bonds? Daniel Roe
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Elisa Frezza
- Re: [AMBER] hydrogen bond analysis Daniel Roe
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Daniel Roe
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Elisa Frezza
- [AMBER] is the 'image' behavior of cpptraj's 'distance' command correct? Jan-Philip Gehrcke
- Re: [AMBER] vacuum simulation fails using pmemd Jason Swails
- Re: [AMBER] is the 'image' behavior of cpptraj's 'distance' command correct? Daniel Roe
- [AMBER] AMBER GPU "Success Stories" mark94025.comcast.net
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Daniel Roe
- Re: [AMBER] warning during nmode calulation - Not all of your snapshots minimized within tolerable limits for nmode Bill Miller III
- Re: [AMBER] Ion clumping in large protein-RNA systems Kamali Sripathi
- Re: [AMBER] Problem while running MMPBSA qiqi
- Re: [AMBER] Ion clumping in large protein-RNA systems Kevin Hauser
- Re: [AMBER] Issues with library location on compiling AmberTools12 David A. Case
- Re: [AMBER] (no subject) David A. Case
- Re: [AMBER] Problem while running MMPBSA Jason Swails
- Re: [AMBER] Issues with library location on compiling AmberTools12 Francesco Pietra
Saturday, 23 June 2012
- [AMBER] Question on Ig=-1 usage Dilraj LAMA
- Re: [AMBER] How to explain this phenomenon is production MD Acoot Brett
- [AMBER] How does 'restraint' work in Amber? Adam Jion
- Re: [AMBER] How does 'restraint' work in Amber? vishal kumar Jaiswal
- Re: [AMBER] How does 'restraint' work in Amber? vishal kumar Jaiswal
- Re: [AMBER] How to explain this phenomenon is production MD steinbrt.rci.rutgers.edu
- [AMBER] Mn2+ parameter Indrajit Deb
- [AMBER] Making a complex Saaz Sakrikar
- Re: [AMBER] Question on Ig=-1 usage David A. Case
- Re: [AMBER] Making a complex David A. Case
- [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht
- Re: [AMBER] vacuum simulation fails using pmemd g t
- [AMBER] Fwd: Mn2+ parameter and crystal water Indrajit Deb
- Re: [AMBER] How to explain this phenomenon is production MD Acoot Brett
- Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Ben Roberts
Sunday, 24 June 2012
- [AMBER] the problem of cpptraj xiaojiong
- Re: [AMBER] the problem of cpptraj Jason Swails
- Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht
- [AMBER] Pressure Regulaton Under Position Restraint Adam Jion
- Re: [AMBER] How to explain this phenomenon is production MD steinbrt.rci.rutgers.edu
- [AMBER] Re [amber] north/sout energy difference Steven M. Graham
- [AMBER] Problem in MM-PBSA decomp module moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] Re [amber] north/sout energy difference Jiri Sponer
- Re: [AMBER] Problem in MM-PBSA decomp module Jason Swails
Monday, 25 June 2012
- [AMBER] problem in antechamber jit mukherjee
- Re: [AMBER] is the 'image' behavior of cpptraj's 'distance' command correct? Jan-Philip Gehrcke
- Re: [AMBER] problem in antechamber David A Case
- Re: [AMBER] Pressure Regulaton Under Position Restraint David A Case
- Re: [AMBER] Fwd: Mn2+ parameter and crystal water David A Case
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! David A Case
- [AMBER] Doubt about ligand preparation in Gaussian and tleap Jitesh Doshi
- [AMBER] binding energy of duplex DNA by mm-pbsa barb fr
- Re: [AMBER] Doubt about ligand preparation in Gaussian and tleap David A Case
- Re: [AMBER] Problem while running MMPBSA qiqi
- Re: [AMBER] binding energy of duplex DNA by mm-pbsa David A Case
- Re: [AMBER] binding energy of duplex DNA by mm-pbsa Ilyas Yildirim
- [AMBER] problem in running LES calculation with a solvated shell system Sajeewa Pemasinghe
- [AMBER] REMD structure failure Do Yong Kim
- Re: [AMBER] REMD structure failure Carlos Simmerling
- Re: [AMBER] Problem while running MMPBSA Jason Swails
- Re: [AMBER] R: strange POPC under lipids 11 FF Benjamin Madej
- Re: [AMBER] force field library for protonated cytosine Asmita Gupta
- [AMBER] AmberTools 12 pbsa: missing newline character in OpenDX output Jan-Philip Gehrcke
- [AMBER] Fwd: AmberTools 12 pbsa: missing newline character in OpenDX output Ray Luo, Ph.D.
- Re: [AMBER] R: strange POPC under lipids 11 FF Albert
- Re: [AMBER] (no subject) DEBOSTUTI GHOSHDASTIDAR
- Re: [AMBER] force field library for protonated cytosine David A Case
- Re: [AMBER] R: strange POPC under lipids 11 FF Benjamin Madej
- Re: [AMBER] force field library for protonated cytosine Asmita Gupta
- Re: [AMBER] (no subject) Jason Swails
- [AMBER] valence not found for for [Na+ ] Mahendra B Thapa
- [AMBER] creating a bellymask which includes residues at a given distance from a point Sajeewa Pemasinghe
- Re: [AMBER] creating a bellymask which includes residues at a given distance from a point Jason Swails
- [AMBER] using bellymask and group specification together Sajeewa Pemasinghe
- Re: [AMBER] force field library for protonated cytosine case
- Re: [AMBER] using bellymask and group specification together case
- Re: [AMBER] valence not found for for [Na+ ] Daniel Roe
- [AMBER] Fwd: problem in running LES calculation with a solvated shell system Sajeewa Pemasinghe
- Re: [AMBER] (no subject) DEBOSTUTI GHOSHDASTIDAR
Tuesday, 26 June 2012
- Re: [AMBER] Doubt about ligand preparation in Gaussian and tleap FyD
- [AMBER] Reading velocities from netcdf file Hemant Gangwar
- [AMBER] problem in the bondtype judgement step in antechamber jit mukherjee
- Re: [AMBER] force field library for protonated cytosine FyD
- [AMBER] Can we change BUFFER_SIZE (1024) ? kurisaki
- Re: [AMBER] Fwd: Mn2+ parameter and crystal water Indrajit Deb
- Re: [AMBER] problem in the bondtype judgement step in antechamber FyD
- [AMBER] Reading velocities from netcdf file Hemant Gangwar
- Re: [AMBER] problem in the bondtype judgement step in antechamber jit mukherjee
- Re: [AMBER] problem in running LES calculation with a solvated shell system Carlos Simmerling
- [AMBER] Fwd: HIMANSHU JOSHI
- [AMBER] PTRAJ not able to read netcdf format HIMANSHU JOSHI
- [AMBER] Implicit solvent (GB options) with GLYCAM_06h Kepa K. Burusco
- [AMBER] calculation of the average structure Olena Dobrovolska
- Re: [AMBER] problem in running LES calculation with a solvated shell system Sajeewa Pemasinghe
- Re: [AMBER] problem in running LES calculation with a solvated shell system Carlos Simmerling
- Re: [AMBER] calculation of the average structure Jason Swails
- Re: [AMBER] PTRAJ not able to read netcdf format Jason Swails
- Re: [AMBER] Can we change BUFFER_SIZE (1024) ? Jason Swails
- Re: [AMBER] calculation of the average structure Olena Dobrovolska
- Re: [AMBER] calculation of the average structure Jason Swails
- [AMBER] using "append" in trajout Mahendra B Thapa
- Re: [AMBER] Implicit solvent (GB options) with GLYCAM_06h Lachele Foley (Lists)
- Re: [AMBER] parameters for Lys-sugar Lachele Foley (Lists)
- Re: [AMBER] parameters for Lys-sugar Urszula Uciechowska
- Re: [AMBER] Implicit solvent (GB options) with GLYCAM_06h Kepa K. Burusco
- Re: [AMBER] binding energy of duplex DNA by mm-pbsa cieplak.cgl.ucsf.edu
- [AMBER] implicit GB model for membrane simulation houcemeddine othman
- Re: [AMBER] implicit GB model for membrane simulation Ray Luo, Ph.D.
- Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht
- Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 case
- Re: [AMBER] Can we change BUFFER_SIZE (1024) ? kurisaki
- [AMBER] AMBER Error: unable to achieve consistency Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] AMBER Error: unable to achieve consistency Ross Walker
- Re: [AMBER] AMBER Error: unable to achieve consistency Asma Abro 28-FBAS/MSBI/F09
- Re: [AMBER] AMBER Error: unable to achieve consistency Asma Abro 28-FBAS/MSBI/F09
- [AMBER] APPEND option does not work in TRAJOUT of CPPTRAJ kurisaki
- Re: [AMBER] APPEND option does not work in TRAJOUT of CPPTRAJ kurisaki
- Re: [AMBER] AMBER Error: unable to achieve consistency Asma Abro 28-FBAS/MSBI/F09
- [AMBER] PMEMD CUPA MPI STOP WRITING OUTPUT IN RUNNIG STATUS HIMANSHU JOSHI
Wednesday, 27 June 2012
- [AMBER] MMPBSA calculation of DNA solvation Soumya Lipsa Rath
- Re: [AMBER] APPEND option does not work in TRAJOUT of CPPTRAJ Jason Swails
- [AMBER] gaff.dat column and preference to frcmod file params Jio M
- Re: [AMBER] MMPBSA calculation of DNA solvation David A Case
- Re: [AMBER] gaff.dat column and preference to frcmod file params David A Case
- Re: [AMBER] gaff.dat column and preference to frcmod file params Jio M
- Re: [AMBER] using "append" in trajout Daniel Roe
- Re: [AMBER] AMBER Error: unable to achieve consistency Jodi Ann Hadden
- Re: [AMBER] PMEMD CUPA MPI STOP WRITING OUTPUT IN RUNNIG STATUS Ross Walker
- Re: [AMBER] PMEMD CUPA MPI STOP WRITING OUTPUT IN RUNNIG STATUS HIMANSHU JOSHI
- [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? Brandon Sim
- Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? Brandon Sim
- Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? Brandon Sim
- Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? David A Case
- Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? Brandon Sim
- [AMBER] MMPBSA.py gbsa unrecognized E. Nihal Korkmaz
- Re: [AMBER] MMPBSA.py gbsa unrecognized Jason Swails
- Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Bill Ross
- [AMBER] a question on molecular dynamics simulation of key residue mutated protein Acoot Brett
- Re: [AMBER] a question on molecular dynamics simulation of key residue mutated protein Carlos Simmerling
- [AMBER] Which server can give the series of PDB files for the energy equivalent conformations Acoot Brett
- Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? case
- Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? Jason Swails
- Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? Brandon Sim
- Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? Jason Swails
- Re: [AMBER] AMBER Error: unable to achieve consistency Asma Abro 28-FBAS/MSBI/F09
- [AMBER] all_prot_nucleic10.lib file in amber12 Asmita Gupta
- [AMBER] Monitoring formation of Water bridges in ptraj Andre Serobian
- Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? Brandon Sim
- Re: [AMBER] all_prot_nucleic10.lib file in amber12 FyD
Thursday, 28 June 2012
- Re: [AMBER] warning during nmode calulation - Not all of your snapshots minimized within tolerable limits for nmode Sangita Kachhap
- Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht
- Re: [AMBER] Problem while running MMPBSA qiqi
- Re: [AMBER] AMBER Error: unable to achieve consistency Jodi Ann Hadden
- Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 David A Case
- Re: [AMBER] AMBER Error: unable to achieve consistency David A Case
- [AMBER] set box problem Jio M
- Re: [AMBER] force field library for protonated cytosine Jio M
- Re: [AMBER] force field library for protonated cytosine David A Case
- [AMBER] Low POPC area per lipid - LIPID11 James Murdock
- Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht
- [AMBER] rmsd Wilson, Katie
- Re: [AMBER] rmsd Carlos Simmerling
- Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Ross Walker
- Re: [AMBER] Low POPC area per lipid - LIPID11 Ross Walker
- Re: [AMBER] rmsd Wilson, Katie
- Re: [AMBER] rmsd Carlos Simmerling
- Re: [AMBER] rmsd Wilson, Katie
- Re: [AMBER] rmsd Carlos Simmerling
- Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht
- [AMBER] REMD trajectories: Ts -> replicas panecka.icm.edu.pl
- Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Jason Swails
- Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Ross Walker
- Re: [AMBER] rmsd Wilson, Katie
- [AMBER] Prepgen omits information about half of the atoms Maria Minakova
- Re: [AMBER] rmsd Niel Henriksen
- Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht
- Re: [AMBER] Prepgen omits information about half of the atoms Ross Walker
- [AMBER] Re [amber] north/sout energy difference Steven M. Graham
- Re: [AMBER] Re [amber] north/sout energy difference Ilyas Yildirim
- Re: [AMBER] AMBER Error: unable to achieve consistency Asma Abro 28-FBAS/MSBI/F09
Friday, 29 June 2012
- Re: [AMBER] CHAMBER with RNA BERGY
- [AMBER] How to estimate Tm of DNA duplex? Xioling Chuang
- [AMBER] sander termination upon reaching end temperature Brandon Sim
- Re: [AMBER] sander termination upon reaching end temperature Vishal Kumar Jaiswal
- Re: [AMBER] sander termination upon reaching end temperature Carlos Simmerling
- Re: [AMBER] sander termination upon reaching end temperature Brandon Sim
- Re: [AMBER] sander termination upon reaching end temperature Carlos Simmerling
- Re: [AMBER] sander termination upon reaching end temperature Brandon Sim
- Re: [AMBER] sander termination upon reaching end temperature Carlos Simmerling
- [AMBER] no hydrogen added with xleap houcemeddine othman
- Re: [AMBER] no hydrogen added with xleap Vishal Kumar Jaiswal
- Re: [AMBER] sander termination upon reaching end temperature Vishal Kumar Jaiswal
- Re: [AMBER] sander termination upon reaching end temperature Vishal Kumar Jaiswal
- Re: [AMBER] sander termination upon reaching end temperature Carlos Simmerling
- Re: [AMBER] no hydrogen added with xleap houcemeddine othman
- Re: [AMBER] no hydrogen added with xleap David A Case
- [AMBER] update for POPE test Albert
- [AMBER] update for POPE test Albert
- Re: [AMBER] update for POPE test Vlad Cojocaru
- Re: [AMBER] update for POPE test Åge Skjevik
- Re: [AMBER] update for POPE test Sarah Witzke
- [AMBER] Fw: set box problem Jio M
- [AMBER] set box problem: not solved Jio M
- Re: [AMBER] Fw: set box problem David A Case
- [AMBER] atom type specification for chlorine Sanjib Paul
- Re: [AMBER] update for POPE test Albert
- Re: [AMBER] update for POPE test Åge Skjevik
- [AMBER] trajectory imaging results in structural clashes in protein-ligand complexes Harald Lanig
- Re: [AMBER] trajectory imaging results in structural clashes in protein-ligand complexes Carlos Simmerling
- Re: [AMBER] Fw: set box problem David A Case
- Re: [AMBER] Re [amber] north/sout energy difference Steven M. Graham
- Re: [AMBER] Re [amber] north/sout energy difference Ilyas Yildirim
- Re: [AMBER] Problem while running MMPBSA qiqi
- Re: [AMBER] sander termination upon reaching end temperature Brandon Sim
- Re: [AMBER] sander termination upon reaching end temperature Ross Walker
- Re: [AMBER] Fw: set box problem Jio M
Saturday, 30 June 2012
- [AMBER] How to call up ptraj in supercomputer facilities? should I use mpi? Catein Catherine
- [AMBER] Amber: mm_pbsa.pl rajeevy.iitk.ac.in
- Re: [AMBER] atom type specification for chlorine case
- [AMBER] Salt concentration: general question Anselm Horn
- Re: [AMBER] Amber: mm_pbsa.pl Ray Luo, Ph.D.
- Re: [AMBER] Salt concentration: general question Carlos Simmerling
- Re: [AMBER] sander termination upon reaching end temperature Brandon Sim

Last message date: Sat Jun 30 2012 - 15:30:03 PDT
Archived on: Fri Nov 22 2024 - 05:54:32 PST

Amber Archive Jun 2012 by date