Amber Archive Sep 2016: by date

Wednesday, 31 August 2016
- Re: [AMBER] change the atom charge in a restart simulations windy
- Re: [AMBER] Regarding the use of sed command to replace water MOHD HOMAIDUR RAHMAN
Thursday, 1 September 2016
- [AMBER] Fwd: MD stop at different time period without giving any error Garima Singh
- Re: [AMBER] changing atom type Jacopo Sgrignani
- Re: [AMBER] Regarding the use of sed command to replace water David A Case
- Re: [AMBER] Fwd: MD stop at different time period without giving any error David A Case
- [AMBER] error in sander minimization Prayagraj Fandilolu
- [AMBER] how to center a polipeptide inside a solvent box Elisa Pieri
- [AMBER] Unable to find mopac charges in mopac.out Sneha Rai
- Re: [AMBER] Unable to find mopac charges in mopac.out Marcelo Andrade Chagas
- Re: [AMBER] autocorr of hydrogen bonds Osman, Roman
- Re: [AMBER] autocorr of hydrogen bonds Roitberg,Adrian E
- Re: [AMBER] autocorr of hydrogen bonds David A Case
- Re: [AMBER] error in sander minimization David A Case
- Re: [AMBER] Unable to find mopac charges in mopac.out Sneha Rai
- Re: [AMBER] Unable to find mopac charges in mopac.out Hannes Loeffler
- Re: [AMBER] Unable to find mopac charges in mopac.out Sneha Rai
- [AMBER] noshakemask and qmshake Fabrício Bracht
- Re: [AMBER] Unable to find mopac charges in mopac.out Marcelo Andrade Chagas
- Re: [AMBER] Unable to find mopac charges in mopac.out David A Case
- [AMBER] radial distribution function from 1drism calculation Jingyi Yan
- Re: [AMBER] radial distribution function from 1drism calculation Tyler Luchko (Lists)
- [AMBER] Any idea about this Amber compile bug? David Cerutti
- [AMBER] accelerated MD Neha Gandhi
- Re: [AMBER] how to center a polipeptide inside a solvent box Jason Swails
- Re: [AMBER] Any idea about this Amber compile bug? Jason Swails
- Re: [AMBER] Any idea about this Amber compile bug? Scott Brozell
- [AMBER] QMMM simulation with user-specified basis set in amber zycz138.126.com
- Re: [AMBER] Unable to find mopac charges in mopac.out Ashutosh Shandilya
Friday, 2 September 2016
- Re: [AMBER] Unable to find mopac charges in mopac.out Sneha Rai
- [AMBER] Fwd: File redirection commands with targeted MD Sonia Ziada
- [AMBER] query regaridng unrestarint minimization step Saman Yousuf ali
- [AMBER] Which is the best thermostat for cMD? Dd H
- Re: [AMBER] Question about QM/MM Anna Cebrian Prats
- [AMBER] RMS-fit during PCA Anasuya Dighe
- Re: [AMBER] how to center a polipeptide inside a solvent box Elisa Pieri
- Re: [AMBER] Unable to find mopac charges in mopac.out David A Case
- Re: [AMBER] how to center a polipeptide inside a solvent box David A Case
- Re: [AMBER] error in sander minimization Prayagraj Fandilolu
- [AMBER] Trajectory analysis Anna Cebrian Prats
- Re: [AMBER] Question about QM/MM Adrian Roitberg
- Re: [AMBER] RMS-fit during PCA Hai Nguyen
- Re: [AMBER] Question about QM/MM Gustavo Seabra
- Re: [AMBER] Trajectory analysis Hai Nguyen
- Re: [AMBER] Question about QM/MM Fabrício Bracht
- Re: [AMBER] Question about QM/MM Adrian Roitberg
- Re: [AMBER] Question about QM/MM Fabrício Bracht
- Re: [AMBER] Question about QM/MM Adrian Roitberg
- Re: [AMBER] Question about QM/MM Fabrício Bracht
- Re: [AMBER] Question about QM/MM Adrian Roitberg
- Re: [AMBER] Question about QM/MM Fabrício Bracht
- Re: [AMBER] Question about QM/MM Adrian Roitberg
- Re: [AMBER] Question about QM/MM Marc van der Kamp
Saturday, 3 September 2016
- [AMBER] lig.frcmod file is not formed Vishal Nemaysh
Sunday, 4 September 2016
- [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 sunyeping
- Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 Bill Ross
- [AMBER] Hydrophobic interactions in MM-GBSA Atila Petrosian
- Re: [AMBER] Hydrophobic interactions in MM-GBSA Carlos Simmerling
- Re: [AMBER] Hydrophobic interactions in MM-GBSA Atila Petrosian
- Re: [AMBER] Hydrophobic interactions in MM-GBSA Nhai
- Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 David A Case
- Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 sunyeping
- Re: [AMBER] Hydrophobic interactions in MM-GBSA Carlos Simmerling
- Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 Bill Ross
- [AMBER] Parmed.py, deleteBond and setBond Aronica, Pietro
- Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 sunyeping
- Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 Bill Ross
Monday, 5 September 2016
- [AMBER] Fwd: lig.frcmod file is not formed Vishal Nemaysh
- [AMBER] Select a snapshot Anna Cebrian Prats
- Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 sunyeping
- [AMBER] Temperature connected to the dipole convergence in the output BLEY Michael
- Re: [AMBER] GROMACS File Conversion Subtlety Mark Abraham
- [AMBER] historical changes to LYN charges in amber03 Mark Abraham
- Re: [AMBER] historical changes to LYN charges in amber03 Carlos Simmerling
- Re: [AMBER] historical changes to LYN charges in amber03 Mark Abraham
- Re: [AMBER] Question about QM/MM Anna Cebrian Prats
- Re: [AMBER] historical changes to LYN charges in amber03 Carlos Simmerling
- Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 Bill Ross
- Re: [AMBER] historical changes to LYN charges in amber03 David A Case
- Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 Jason Swails
- Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 Bill Ross
- Re: [AMBER] Select a snapshot Daniel Roe
- [AMBER] How to fixed residues in amber? windy
Tuesday, 6 September 2016
- Re: [AMBER] Question about QM/MM David A Case
- Re: [AMBER] How to fixed residues in amber? David A Case
- [AMBER] resp charges in LIPID14 jojartb.jgypk.u-szeged.hu
- Re: [AMBER] Checking AmberTools16 installation Bence Hégely
- Re: [AMBER] Checking AmberTools16 installation David A Case
- Re: [AMBER] Question about QM/MM Anna Cebrian Prats
- Re: [AMBER] Which is the best thermostat for cMD? David A Case
- Re: [AMBER] resp charges in LIPID14 Dickson, Callum J
- Re: [AMBER] Temperature connected to the dipole convergence in the output David A Case
- Re: [AMBER] historical changes to LYN charges in amber03 Mark Abraham
- Re: [AMBER] Question about QM/MM Adrian Roitberg
- Re: [AMBER] Question about QM/MM Anna Cebrian Prats
- Re: [AMBER] Question about QM/MM Adrian Roitberg
- [AMBER] about print_res in MMPBSA.py Thomas Evangelidis
- [AMBER] [Amber] Periodic Box Issue Chase Zagorec-Marks
- Re: [AMBER] [Amber] Periodic Box Issue Adrian Roitberg
- Re: [AMBER] [Amber] Periodic Box Issue Chase Zagorec-Marks
- Re: [AMBER] about print_res in MMPBSA.py Jason Swails
- Re: [AMBER] about print_res in MMPBSA.py Thomas Evangelidis
- Re: [AMBER] about print_res in MMPBSA.py Jason Swails
- [AMBER] query regarding radial distribution function plot. Saman Yousuf ali
- Re: [AMBER] query regarding radial distribution function plot. Daniel Roe
- Re: [AMBER] Which is the best thermostat for cMD? Dd H
- [AMBER] MMPBSA analysis for a heme protein Smriti Sharma
Wednesday, 7 September 2016
- [AMBER] How to assign frame range for cpptraj analysis? sunyeping
- [AMBER] Problem with MCPB.py workflow after calculation of force constants. Abhi Acharya
- Re: [AMBER] How to assign frame range for cpptraj analysis? Anna Cebrian Prats
- Re: [AMBER] How to assign frame range for cpptraj analysis? sunyeping
- Re: [AMBER] MMPBSA analysis for a heme protein David A Case
- Re: [AMBER] Question about QM/MM Anna Cebrian Prats
- Re: [AMBER] Problem with MCPB.py workflow after calculation of force constants. Marcelo Andrade Chagas
- [AMBER] changepot Xiaoliu Zhang
- Re: [AMBER] changepot Adrian Roitberg
- [AMBER] distance based mask Kris Feher
- Re: [AMBER] distance based mask Daniel Roe
- Re: [AMBER] distance based mask Kris Feher
- [AMBER] Switching from PM3-PDDG to SCC-DFT method Thakur, Abhishek
- Re: [AMBER] Switching from PM3-PDDG to SCC-DFT method Adrian Roitberg
Thursday, 8 September 2016
- [AMBER] Upgrade AMBER 14 to 16 Anton Perera
- [AMBER] On the simulation of phosphate ions in water solution Casalini Tommaso
- [AMBER] question on the reference data of GIST Shunsuke Mizutani
- [AMBER] Radial Distribution Function Fatema Al-Haddad [fy14fmah]
- Re: [AMBER] Upgrade AMBER 14 to 16 David A Case
- Re: [AMBER] question on the reference data of GIST David A Case
- Re: [AMBER] Radial Distribution Function David A Case
- Re: [AMBER] autoimage bug? Filip Persson
- Re: [AMBER] autoimage bug? Filip Persson
- Re: [AMBER] Fwd: File redirection commands with targeted MD Sonia Ziada
- Re: [AMBER] Fwd: File redirection commands with targeted MD Carlos Simmerling
- Re: [AMBER] Fwd: File redirection commands with targeted MD Sonia Ziada
- Re: [AMBER] Fwd: File redirection commands with targeted MD Florent Barbault
- Re: [AMBER] Fwd: File redirection commands with targeted MD Sonia Ziada
- Re: [AMBER] Problem with MCPB.py workflow after calculation of force constants. Pengfei Li
- Re: [AMBER] question on the reference data of GIST Tom Kurtzman
- [AMBER] Problem with CRD files dhanasekar.mbu.iisc.ernet.in
- Re: [AMBER] Fwd: File redirection commands with targeted MD Bill Ross
- Re: [AMBER] Problem with CRD files Nhai
- Re: [AMBER] Problem with CRD files Nhai
- Re: [AMBER] On the simulation of phosphate ions in water solution Niel Henriksen
Friday, 9 September 2016
- Re: [AMBER] Fwd: File redirection commands with targeted MD Michael Shokhen
- [AMBER] PME calculation for Vacuum? Mochena, Mogus D.
- Re: [AMBER] PME calculation for Vacuum? Bill Ross
- Re: [AMBER] PME calculation for Vacuum? Charles Lin
- Re: [AMBER] PME calculation for Vacuum? Mochena, Mogus D.
- Re: [AMBER] PME calculation for Vacuum? Bill Ross
- Re: [AMBER] PME calculation for Vacuum? Bill Ross
- [AMBER] generating topology file for non-standard amino acid Chitrak Gupta
Saturday, 10 September 2016
- Re: [AMBER] PME calculation for Vacuum? David A Case
- Re: [AMBER] PME calculation for Vacuum? Mochena, Mogus D.
- Re: [AMBER] generating topology file for non-standard amino acid David A Case
- [AMBER] Calculations of dG for protein-ions James Starlight
- [AMBER] lipid bilayer Sofia Vasilakaki
- [AMBER] Add Molecule symmetry to sander tanfei777.sina.cn
Sunday, 11 September 2016
- [AMBER] Speed issue with Accelerated molecular dynamics. Abhilash J
- Re: [AMBER] Speed issue with Accelerated molecular dynamics. Marc van der Kamp
- Re: [AMBER] Speed issue with Accelerated molecular dynamics. Abhilash J
- [AMBER] PCA plotting waleed zalloum
- Re: [AMBER] Add Molecule symmetry to sander Carlos Simmerling
- [AMBER] 回复：Re: Add Molecule symmetry to sander tanfei777.sina.cn
- [AMBER] 回复： Enforced Symmetry? tanfei777.sina.cn
- [AMBER] Problems about creating ligand leap input files 康宁
- Re: [AMBER] Problems about creating ligand leap input files Bill Ross
Monday, 12 September 2016
- [AMBER] cpptraj Beale, John
- Re: [AMBER] cpptraj Bill Ross
- [AMBER] MMPBSA with different external Dielectric Constant Elvis Martis
- Re: [AMBER] MMPBSA with different external Dielectric Constant Jason Swails
- Re: [AMBER] PCA plotting Jason Swails
- [AMBER] cpinutil.py describe flag Elisa Pieri
- Re: [AMBER] cpinutil.py describe flag Jason Swails
- Re: [AMBER] MMPBSA with different external Dielectric Constant Adrian Roitberg
- Re: [AMBER] cpinutil.py describe flag Elisa Pieri
- [AMBER] pmemd Segmentation fault on Tutorial A27 liu junjun
- [AMBER] SCC-DFTB Thakur, Abhishek
- Re: [AMBER] SCC-DFTB Adrian Roitberg
- Re: [AMBER] cpptraj Daniel Roe
- [AMBER] NVIDIA GTX-970 Class Action Suit $30 settlement link Ross Walker
- Re: [AMBER] cpinutil.py describe flag Jason Swails
- Re: [AMBER] pmemd Segmentation fault on Tutorial A27 liu junjun
- [AMBER] bad atom type: Mn Thomas Evangelidis
- Re: [AMBER] MMPBSA with different external Dielectric Constant Elvis Martis
- Re: [AMBER] MMPBSA with different external Dielectric Constant Jason Swails
- [AMBER] How by residue decomposition in MMPBSA.py is performed? Irina Ivanova
- [AMBER] comparing pytraj vs. sander output Niel Henriksen
- Re: [AMBER] comparing pytraj vs. sander output Hai Nguyen
Tuesday, 13 September 2016
- Re: [AMBER] comparing pytraj vs. sander output Jason Swails
- [AMBER] Error: cannot run "/share/apps/amber/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit shahab shariati
- Re: [AMBER] Error: cannot run "/share/apps/amber/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit shahab shariati
- Re: [AMBER] Error: cannot run "/share/apps/amber/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit shahab shariati
- Re: [AMBER] How by residue decomposition in MMPBSA.py is performed? Jason Swails
- Re: [AMBER] 回复：Re: Add Molecule symmetry to sander Jason Swails
- [AMBER] Fullerene RESP charges derivation Fabio Bologna
- Re: [AMBER] comparing pytraj vs. sander output Niel Henriksen
- Re: [AMBER] comparing pytraj vs. sander output Nhai
- Re: [AMBER] comparing pytraj vs. sander output Daniel Roe
- Re: [AMBER] comparing pytraj vs. sander output Niel Henriksen
- Re: [AMBER] comparing pytraj vs. sander output Daniel Roe
- Re: [AMBER] comparing pytraj vs. sander output Hai Nguyen
- Re: [AMBER] comparing pytraj vs. sander output Jason Swails
- Re: [AMBER] comparing pytraj vs. sander output Hai Nguyen
- Re: [AMBER] comparing pytraj vs. sander output Hai Nguyen
- Re: [AMBER] comparing pytraj vs. sander output Niel Henriksen
- Re: [AMBER] comparing pytraj vs. sander output Hai Nguyen
- Re: [AMBER] comparing pytraj vs. sander output Niel Henriksen
- Re: [AMBER] comparing pytraj vs. sander output Jason Swails
- Re: [AMBER] Error: cannot run "/share/apps/amber/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit Samuel Bowerman
- [AMBER] FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type. Failed to generate parameters Parameter file was not saved. shahab shariati
- [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations hari krishna
- [AMBER] Fwd: query with amber Pooja Kesari
- Re: [AMBER] FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type. Failed to generate parameters Parameter file was not saved. Bill Ross
- Re: [AMBER] Fwd: query with amber Bill Ross
Wednesday, 14 September 2016
- Re: [AMBER] Fwd: query with amber Pooja Kesari
- Re: [AMBER] Fwd: query with amber Bill Ross
- Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations Carlos Simmerling
- [AMBER] How to "not" strip an ion (say Mg) in MMPBSA Hirdesh Kumar
- [AMBER] Force field ff14SB Anna Cebrian Prats
- Re: [AMBER] Fullerene RESP charges derivation David A Case
- Re: [AMBER] FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type. Failed to generate parameters Parameter file was not saved. David A Case
- Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations David A Case
- Re: [AMBER] Fwd: query with amber David A Case
- [AMBER] R: Fullerene RESP charges derivation Fabio Bologna
- [AMBER] Parameters for GppNHp ligand. Dd H
- Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations Vlad Cojocaru
- Re: [AMBER] How to "not" strip an ion (say Mg) in MMPBSA Bruno Falcone
- Re: [AMBER] How to "not" strip an ion (say Mg) in MMPBSA Jason Swails
- Re: [AMBER] Force field ff14SB Jason Swails
- Re: [AMBER] Force field ff14SB Carlos Simmerling
- Re: [AMBER] Force field ff14SB Anna Cebrian Prats
- Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations hari krishna
- Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations Jiri Sponer
- [AMBER] Potential Energy in 3D-RISM Maksim Mišin
- Re: [AMBER] FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type. Failed to generate parameters Parameter file was not saved. Yeng-Tseng Wang
- Re: [AMBER] Potential Energy in 3D-RISM Tyler Luchko (Lists)
- Re: [AMBER] Fwd: query with amber Pooja Kesari
- Re: [AMBER] Fwd: query with amber Bill Ross
- [AMBER] Problem with CRD files dhanasekar.mbu.iisc.ernet.in
Thursday, 15 September 2016
- [AMBER] Glaycam04 version for q4md-CD FF Helen Lvy
- Re: [AMBER] Problem with CRD files Hai Nguyen
- [AMBER] Continue a simulation run Pooja Kesari
- Re: [AMBER] Continue a simulation run Bilal Nizami
- [AMBER] WARNING: The unperturbed charge of the unit: -0.99 is not zero. shahab shariati
- [AMBER] changeLJPair/pmemd.cuda Batuhan Kav
- [AMBER] Follow up Mochena, Mogus D.
- [AMBER] DNA residue atom names. Christian Schafmeister
- [AMBER] hbond and autoimage Francesco Gentile
Friday, 16 September 2016
- Re: [AMBER] Continue a simulation run David A Case
- Re: [AMBER] WARNING: The unperturbed charge of the unit: -0.99 is not zero. David A Case
- Re: [AMBER] changeLJPair/pmemd.cuda David A Case
- Re: [AMBER] Follow up David A Case
- Re: [AMBER] DNA residue atom names. David A Case
- Re: [AMBER] Problem with CRD files dhanasekar.mbu.iisc.ernet.in
- Re: [AMBER] Continue a simulation run Pooja Kesari
- [AMBER] aromatic ring plane distorted Thomas Evangelidis
- Re: [AMBER] aromatic ring plane distorted Carlos Simmerling
- Re: [AMBER] hbond and autoimage Daniel Roe
- Re: [AMBER] aromatic ring plane distorted Thomas Evangelidis
- Re: [AMBER] aromatic ring plane distorted Bill Ross
- Re: [AMBER] Continue a simulation run Hai Nguyen
- [AMBER] "ATTN, need revision" in frcmod file / Could not find bond parameter & Could not find angle parameter shahab shariati
- Re: [AMBER] "ATTN, need revision" in frcmod file / Could not find bond parameter & Could not find angle parameter ABEL Stephane 175950
- Re: [AMBER] "ATTN, need revision" in frcmod file / Could not find bond parameter & Could not find angle parameter Hannes Loeffler
- Re: [AMBER] DNA residue atom names. Bill Ross
- [AMBER] How to get GppNHp parameters. Dd H
Saturday, 17 September 2016
- [AMBER] Simulation of protein complex with four protein chains Jag Silwal
- [AMBER] AMBER installation help Huma Tahir
- [AMBER] Installing amber tools on ubuntu neelam wafa
- Re: [AMBER] AMBER installation help Bill Ross
- Re: [AMBER] Installing amber tools on ubuntu Bill Ross
- Re: [AMBER] Installing amber tools on ubuntu chandan patel
- Re: [AMBER] AMBER installation help Hai Nguyen
Sunday, 18 September 2016
- Re: [AMBER] AMBER installation help Huma Tahir
- [AMBER] chamber in parmed (Amber16) Song-Ho Chong
- Re: [AMBER] chamber in parmed (Amber16) Jason Swails
- [AMBER] delete residue in tleap Thomas Evangelidis
- Re: [AMBER] delete residue in tleap Bill Ross
- Re: [AMBER] delete residue in tleap Thomas Evangelidis
- Re: [AMBER] delete residue in tleap Bill Ross
- Re: [AMBER] chamber in parmed (Amber16) Song-Ho Chong
Monday, 19 September 2016
- [AMBER] adaptive qm/mm NVT, number of quantum atoms outside the legal range Stregone
- Re: [AMBER] Problem with CRD files Daniel Roe
- Re: [AMBER] autoimage bug? Daniel Roe
- [AMBER] SCC-DFTB Thakur, Abhishek
- [AMBER] Parmchk - missing nitro improper Miha Purg
- Re: [AMBER] adaptive qm/mm NVT, number of quantum atoms outside the legal range Dr. Andreas W. Goetz
- Re: [AMBER] SCC-DFTB Dr. Andreas W. Goetz
Tuesday, 20 September 2016
- Re: [AMBER] Glaycam04 version for q4md-CD FF FyD
- Re: [AMBER] Fullerene RESP charges derivation FyD
- Re: [AMBER] Glaycam04 version for q4md-CD FF Lachele Foley
- Re: [AMBER] Glaycam04 version for q4md-CD FF FyD
- Re: [AMBER] Problem with atommap function in cpptraj (v16) Daniel Roe
- Re: [AMBER] Amber16: COM's in GPU version Carlos Simmerling
- [AMBER] what is DFTB and SCC-DFTB Thakur, Abhishek
- Re: [AMBER] Problem with atommap function in cpptraj (v16) Samuel Bowerman
- Re: [AMBER] Amber16: COM's in GPU version Ross Walker
- Re: [AMBER] Problem with atommap function in cpptraj (v16) Daniel Roe
- [AMBER] fixing concentration in implicit solvent simulation Chitrak Gupta
- Re: [AMBER] Problem with CRD files Daniel Roe
- Re: [AMBER] fixing concentration in implicit solvent simulation Carlos Simmerling
- Re: [AMBER] what is DFTB and SCC-DFTB Marc van der Kamp
- Re: [AMBER] what is DFTB and SCC-DFTB Thakur, Abhishek
- [AMBER] positive electrostatic energy MM-PBSA Trang Nguyen
Wednesday, 21 September 2016
- [AMBER] Parmchk - missing improper parameter for nitro group Miha Purg
- [AMBER] frame wise MMPBSA energy difference Hirdesh Kumar
- [AMBER] DFTB and slater koster files Markus Kaukonen
- Re: [AMBER] positive electrostatic energy MM-PBSA David A Case
- Re: [AMBER] frame wise MMPBSA energy difference Jason Swails
- Re: [AMBER] frame wise MMPBSA energy difference Hirdesh Kumar
- [AMBER] A refresher on how non-bonding terms are represented in a topology file. Christian Schafmeister
- [AMBER] setup time with pmemd.cuda Hannes Loeffler
- Re: [AMBER] setup time with pmemd.cuda Ross Walker
- Re: [AMBER] setup time with pmemd.cuda Hannes Loeffler
- Re: [AMBER] setup time with pmemd.cuda Ross Walker
- Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file. Daniel Roe
- Re: [AMBER] fixing concentration in implicit solvent simulation Chitrak Gupta
- Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file. Christian Schafmeister
- Re: [AMBER] setup time with pmemd.cuda Hannes Loeffler
- [AMBER] Segmentation fault in tleap when using "sequence" command Lane Votapka
- Re: [AMBER] setup time with pmemd.cuda Ross Walker
- Re: [AMBER] Segmentation fault in tleap when using "sequence" command Daniel Roe
- Re: [AMBER] Segmentation fault in tleap when using "sequence" command Daniel Roe
- Re: [AMBER] Segmentation fault in tleap when using "sequence" command Bill Ross
- Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file. Jason Swails
- Re: [AMBER] fixing concentration in implicit solvent simulation Jason Swails
- Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file. David A Case
- Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file. Bill Ross
- [AMBER] dihedral PCA amber Neha Gandhi
- [AMBER] Plot activesite water vs time. Saman Yousuf ali
- Re: [AMBER] Plot activesite water vs time. mmaestre
- Re: [AMBER] Plot activesite water vs time. Saman Yousuf ali
- Re: [AMBER] Plot activesite water vs time. mmaestre
Thursday, 22 September 2016
- [AMBER] Implicit solvent with GPU AMBER and Pulling direction in SMD Ana Bergues
- [AMBER] How to 2D-RDF in cpptraj. Saman Yousuf ali
- [AMBER] Fw:car_to_files.py in AMBER16 is not available. Jinfeng Huang
- Re: [AMBER] setup time with pmemd.cuda Hannes Loeffler
- Re: [AMBER] fixing concentration in implicit solvent simulation David A Case
- Re: [AMBER] setup time with pmemd.cuda Scott Brozell
- Re: [AMBER] Parmchk - missing improper parameter for nitro group David A Case
- Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file. Jason Swails
- Re: [AMBER] Segmentation fault in tleap when using "sequence" command Lane Votapka
- Re: [AMBER] Segmentation fault in tleap when using "sequence" command Lane Votapka
- Re: [AMBER] Segmentation fault in tleap when using "sequence" command Carlos Simmerling
- Re: [AMBER] Segmentation fault in tleap when using "sequence" command Lane Votapka
- [AMBER] Unstable SHAKE ABHIJEET CHOWDHURY
- Re: [AMBER] Segmentation fault in tleap when using "sequence" command Daniel Roe
- Re: [AMBER] Unstable SHAKE Daniel Roe
- Re: [AMBER] Unstable SHAKE Carlos Simmerling
- Re: [AMBER] Unstable SHAKE ABHIJEET CHOWDHURY
- Re: [AMBER] Segmentation fault in tleap when using "sequence" command Lane Votapka
- [AMBER] minimzation & MD in vacuo Thomas Evangelidis
- Re: [AMBER] dihedral PCA amber Daniel Roe
- Re: [AMBER] minimzation & MD in vacuo Thomas Evangelidis
- Re: [AMBER] dihedral PCA amber Neha Gandhi
- Re: [AMBER] dihedral PCA amber Bill Ross
- [AMBER] cpptraj gist core dumped peter.schmidtke.discngine.servier.com
Friday, 23 September 2016
- Re: [AMBER] cpptraj gist core dumped Nhai
- [AMBER] netcdf trajectory Andrew Bostick
- [AMBER] MM-PBSA calculation in different temprature shahab shariati
- Re: [AMBER] dihedral PCA amber Daniel Roe
- Re: [AMBER] netcdf trajectory Daniel Roe
- Re: [AMBER] cpptraj gist core dumped Daniel Roe
- Re: [AMBER] netcdf trajectory David A Case
- Re: [AMBER] MM-PBSA calculation in different temprature Adrian Roitberg
- [AMBER] strip waters using distance criteria Thomas Evangelidis
- Re: [AMBER] MM-PBSA calculation in different temprature shahab shariati
- Re: [AMBER] cpptraj gist core dumped Steven Ramsey
- Re: [AMBER] strip waters using distance criteria Daniel Roe
Saturday, 24 September 2016
- Re: [AMBER] setup time with pmemd.cuda Hannes Loeffler
- [AMBER] How aggressively should bond, angle, torsion parameters be coalesced? Christian Schafmeister
- Re: [AMBER] setup time with pmemd.cuda Daniel Mermelstein
- Re: [AMBER] How aggressively should bond, angle, torsion parameters be coalesced? W. Andeas Svrcek-Seiler
- Re: [AMBER] How aggressively should bond, angle, torsion parameters be coalesced? Christian Schafmeister
- [AMBER] netcdf trajectory Andrew Bostick
- Re: [AMBER] netcdf trajectory Bill Ross
- Re: [AMBER] strip waters using distance criteria Thomas Evangelidis
- Re: [AMBER] netcdf trajectory Hirdesh Kumar
- Re: [AMBER] strip waters using distance criteria Hai Nguyen
Sunday, 25 September 2016
- [AMBER] netcdf trajectory Andrew Bostick
- Re: [AMBER] netcdf trajectory Bill Ross
- Re: [AMBER] netcdf trajectory Bill Ross
- Re: [AMBER] netcdf trajectory Andrew Bostick
- Re: [AMBER] netcdf trajectory TERREUX RAPHAEL
- [AMBER] Signal: Segmentation fault (11) shahab shariati
- [AMBER] Restrain in Umbrella Sampling ATUL KUMAR
- [AMBER] 2 ns heating in constant pH tutorial inquiry Andrew Schaub
- Re: [AMBER] netcdf trajectory Bill Ross
- Re: [AMBER] netcdf trajectory Bill Ross
- Re: [AMBER] netcdf trajectory Jason Swails
- Re: [AMBER] Signal: Segmentation fault (11) David A Case
Monday, 26 September 2016
- [AMBER] create a cubic box of 4.5 nm Jesmita Dhar
- [AMBER] problem about Using ParmEd or xParmEd 杨金鹏
- Re: [AMBER] create a cubic box of 4.5 nm David A Case
- [AMBER] PGI Fortran/C/C++ workstation Hector A. Baldoni
- Re: [AMBER] PGI Fortran/C/C++ workstation Hector A. Baldoni
- Re: [AMBER] netcdf trajectory Kshatresh Dutta Dubey
- [AMBER] pmemd.cuda: multiple bonds illegal for SHAKEH Hannes Loeffler
- Re: [AMBER] problem about Using ParmEd or xParmEd Jason Swails
- Re: [AMBER] pmemd.cuda: multiple bonds illegal for SHAKEH Jason Swails
- Re: [AMBER] 2 ns heating in constant pH tutorial inquiry Jason Swails
- Re: [AMBER] netcdf trajectory Hai Nguyen
- Re: [AMBER] Signal: Segmentation fault (11) shahab shariati
- [AMBER] RESP charge fitting error in MCPB.py zycz138.126.com
- Re: [AMBER] Signal: Segmentation fault (11) David A Case
- Re: [AMBER] dihedral PCA amber Neha Gandhi
Tuesday, 27 September 2016
- [AMBER] Issue regarding parametrization Mahrukh Imtiaz
- Re: [AMBER] Issue regarding parametrization David A Case
- Re: [AMBER] dihedral PCA amber Daniel Roe
- [AMBER] tleap cannot solvate unit in amber16 windy
- Re: [AMBER] tleap cannot solvate unit in amber16 Christina Bergonzo
- [AMBER] Tcl problem Elisa Pieri
- Re: [AMBER] Tcl problem Jason Swails
- Re: [AMBER] Tcl problem Elisa Pieri
- Re: [AMBER] Tcl problem Hai Nguyen
- Re: [AMBER] Tcl problem Jason Swails
- Re: [AMBER] Tcl problem Jason Swails
- [AMBER] Amber NaN error DIAO Jianxiong
- Re: [AMBER] tleap cannot solvate unit in amber16 windy
- Re: [AMBER] autoimage bug? Filip Persson
Wednesday, 28 September 2016
- Re: [AMBER] Tcl problem Elisa Pieri
- [AMBER] Can amber handle carbon -- nitrogen double and single bond? Ming Tang
- Re: [AMBER] Can amber handle carbon -- nitrogen double and single bond? Bill Ross
- Re: [AMBER] dihedral PCA amber Neha Gandhi
- [AMBER] ACS COMP award deadline for Spring 2017 Carlos Simmerling
- [AMBER] mdin for LIO interface Hector A. Baldoni
- [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes. Pooja Kesari
- Re: [AMBER] Signal: Segmentation fault (11) shahab shariati
- Re: [AMBER] Amber NaN error David A Case
- [AMBER] MMPBSA.py error Your ligand residues must be sequential in your complex maryam azimzadehirani
- Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes. David A Case
- Re: [AMBER] autoimage bug? Daniel Roe
- Re: [AMBER] MMPBSA.py error Your ligand residues must be sequential in your complex Dwight McGee
- Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes. Pooja Kesari
- Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes. Nhai
- Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes. David A Case
- Re: [AMBER] Signal: Segmentation fault (11) David A Case
- [AMBER] scaling of mpi version of pmemd.mpi (AMBER14) and that of the MMPBSA.py.MPI Kris Feher
- [AMBER] on periodic conditions and unspecified launch failure Elisa Pieri
- [AMBER] 答复: Amber NaN error DIAO Jianxiong
- [AMBER] FMN parameters ruqaiya khalil
- [AMBER] Disparities in H-bond lifetimes calculated through different approaches Praneeth Bommisetti
- Re: [AMBER] FMN parameters Bill Ross
Thursday, 29 September 2016
- Re: [AMBER] FMN parameters Bill Ross
- [AMBER] Error in the second step using MCPB.py Tiffani Rovira
- Re: [AMBER] FMN parameters ruqaiya khalil
- [AMBER] using boundary information from previous run Hirdesh Kumar
- [AMBER] Pressure of the system during equilibration Debodyuti Dutta
- Re: [AMBER] Disparities in H-bond lifetimes calculated through different approaches Daniel Roe
- Re: [AMBER] Pressure of the system during equilibration Daniel Roe
- Re: [AMBER] using boundary information from previous run Daniel Roe
- Re: [AMBER] on periodic conditions and unspecified launch failure Jason Swails
- Re: [AMBER] scaling of mpi version of pmemd.mpi (AMBER14) and that of the MMPBSA.py.MPI Jason Swails
- Re: [AMBER] on periodic conditions and unspecified launch failure David A Case
- Re: [AMBER] 答复: Amber NaN error David A Case
- Re: [AMBER] using boundary information from previous run David A Case
- [AMBER] Problem regarding sccdftb not converging amitosh gautam
Friday, 30 September 2016
- Re: [AMBER] netcdf trajectory Markowska
- Re: [AMBER] using boundary information from previous run Hirdesh Kumar
- Re: [AMBER] using boundary information from previous run David A Case
- Re: [AMBER] on periodic conditions and unspecified launch failure Elisa Pieri
- Re: [AMBER] LEaP and PARMSETs David A Case
- Re: [AMBER] on periodic conditions and unspecified launch failure Jason Swails
- Re: [AMBER] using boundary information from previous run Hirdesh Kumar
- Re: [AMBER] using boundary information from previous run Daniel Roe
- Re: [AMBER] netcdf trajectory Daniel Roe
- Re: [AMBER] using boundary information from previous run Hirdesh Kumar
- Re: [AMBER] netcdf trajectory Markowska
- Re: [AMBER] using boundary information from previous run David A Case
- Re: [AMBER] Problem regarding sccdftb not converging Thakur, Abhishek
- [AMBER] How to read prmtop file flag pointer section Xiaoyu Wang
- Re: [AMBER] How to read prmtop file flag pointer section Jason Swails
- [AMBER] Save the average structure from two pdb files Iqbal, Muhammad Sajid
- Re: [AMBER] Save the average structure from two pdb files Hai Nguyen
- Re: [AMBER] Error in the second step using MCPB.py Pengfei Li

Last message date: Fri Sep 30 2016 - 20:00:02 PDT
Archived on: Wed Apr 17 2024 - 05:55:17 PDT

Amber Archive Sep 2016 by date