Amber Archive Oct 2014: by date

Tuesday, 30 September 2014
- Re: [AMBER] writing trr trajectory newamber list
- Re: [AMBER] key word to pull out eigenvalues newamber list
Wednesday, 1 October 2014
- [AMBER] LIE FUNCTION Loïc Etheve
- Re: [AMBER] LIE FUNCTION Jason Swails
- Re: [AMBER] writing trr trajectory Daniel Roe
- Re: [AMBER] LIE FUNCTION Jason Swails
- [AMBER] switch from digest amirhossein taghavi
Thursday, 2 October 2014
- [AMBER] RAM error during multiple MMGBSA runs James Starlight
- [AMBER] help: MD on DNA pradeep pant
- Re: [AMBER] help: MD on DNA David A Case
- Re: [AMBER] RAM error during multiple MMGBSA runs Ray Luo, Ph.D.
- Re: [AMBER] switch from digest Jason Swails
Friday, 3 October 2014
- [AMBER] Problems with MMPBSA.py.MPI James Starlight
- Re: [AMBER] RAM error during multiple MMGBSA runs James Starlight
- [AMBER] carbon and nitrogen chemical shift restraints Alexandra Balaceanu
- [AMBER] Cluster RMSD Soumendranath Bhakat
- [AMBER] Processing of the trajectories using ptraj James Starlight
- Re: [AMBER] carbon and nitrogen chemical shift restraints David A Case
- Re: [AMBER] Processing of the trajectories using ptraj Daniel Roe
- [AMBER] help: MD on DNA pradeep pant
- Re: [AMBER] Cluster RMSD Daniel Roe
- [AMBER] QM/MM in amber, PME when qm_theory='extern' Aixiao Li
- Re: [AMBER] help: MD on DNA Jason Swails
- [AMBER] cpptraj Tutorial C1 George Tzotzos
- Re: [AMBER] cpptraj Tutorial C1 George Tzotzos
- Re: [AMBER] cpptraj Tutorial C1 Jason Swails
- Re: [AMBER] cpptraj Tutorial C1 Daniel Roe
- Re: [AMBER] carbon and nitrogen chemical shift restraints Alexandra Balaceanu
Saturday, 4 October 2014
- [AMBER] Tethering water molecules in the receptor George Tzotzos
- Re: [AMBER] Tethering water molecules in the receptor Jason Swails
- Re: [AMBER] Tethering water molecules in the receptor George Tzotzos
- Re: [AMBER] Tethering water molecules in the receptor Jason Swails
Sunday, 5 October 2014
- [AMBER] Langevin thermostat in vacuu simulation o ..High RMSF of TEMP CHAMI F.
- [AMBER] Dummy atom and PMEMD Miroslav Krepl
- Re: [AMBER] Dummy atom and PMEMD Jason Swails
- Re: [AMBER] Langevin thermostat in vacuu simulation o ..High RMSF of TEMP Jason Swails
Monday, 6 October 2014
- Re: [AMBER] Processing of the trajectories using ptraj James Starlight
- Re: [AMBER] Dummy atom and PMEMD Miroslav Krepl
- Re: [AMBER] Dummy atom and PMEMD Jason Swails
- Re: [AMBER] Processing of the trajectories using ptraj Daniel Roe
- [AMBER] Trouble making frcmod file (ultimately to create prmtop file) Evans, Shalton
- Re: [AMBER] Trouble making frcmod file (ultimately to create prmtop file) Jason Swails
- Re: [AMBER] QM/MM in amber, PME when qm_theory='extern' Brian Radak
- Re: [AMBER] Trouble making frcmod file (ultimately to create prmtop file) Brian Radak
Tuesday, 7 October 2014
- [AMBER] On the enthropy estimation in MMPBSA James Starlight
- [AMBER] Chloroform box Neha Gandhi
- [AMBER] Need help for retrained MD Sudhanshu Shanker
- Re: [AMBER] Chloroform box David A Case
- Re: [AMBER] Chloroform box Jason Swails
- Re: [AMBER] Need help for retrained MD Jason Swails
- [AMBER] Fwd: parallel amber installation failed Fabian
- Re: [AMBER] Fwd: parallel amber installation failed Daniel Roe
- Re: [AMBER] Need help for retrained MD Daniel Roe
- Re: [AMBER] Fwd: parallel amber installation failed Fabian Glaser
- Re: [AMBER] Fwd: parallel amber installation failed David A Case
- Re: [AMBER] Fwd: parallel amber installation failed Jason Swails
- Re: [AMBER] Fwd: parallel amber installation failed Jason Swails
- Re: [AMBER] Fwd: parallel amber installation failed Fabian Gmail
- [AMBER] amber12 Installation Error MAC OS X BERGY
- [AMBER] RNA with Malachite Green simulation Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] amber12 Installation Error MAC OS X David A Case
- Re: [AMBER] amber12 Installation Error MAC OS X BERGY
- Re: [AMBER] amber12 Installation Error MAC OS X BERGY
- [AMBER] Lambda Exchange Jeff Wereszczynski
- [AMBER] No AMBERHOME/dat/mtkpp folder mmaestre.gate.sinica.edu.tw
Wednesday, 8 October 2014
- Re: [AMBER] On the enthropy estimation in MMPBSA James Starlight
- Re: [AMBER] No AMBERHOME/dat/mtkpp folder Jason Swails
- Re: [AMBER] No AMBERHOME/dat/mtkpp folder David A Case
- Re: [AMBER] Lambda Exchange Jason Swails
- [AMBER] Regarding dihedrals in GAFF need clarification Arun Srikanth
- Re: [AMBER] Regarding dihedrals in GAFF need clarification Jason Swails
- Re: [AMBER] Regarding dihedrals in GAFF need clarification Arun Srikanth
- Re: [AMBER] Regarding dihedrals in GAFF need clarification Jason Swails
- [AMBER] problems with "Could not find vdW" Investigador Química
- Re: [AMBER] problems with "Could not find vdW" Jason Swails
- Re: [AMBER] problems with "Could not find vdW" Investigador Química
- Re: [AMBER] problems with "Could not find vdW" Jason Swails
- Re: [AMBER] problems with "Could not find vdW" Daniel Roe
- Re: [AMBER] Lambda Exchange Jeff Wereszczynski
- [AMBER] Is there a way to maintain pdb coordinates into leap? Jonathan Gough
- Re: [AMBER] Lambda Exchange Jason Swails
- Re: [AMBER] Is there a way to maintain pdb coordinates into leap? Bill Ross
- Re: [AMBER] Lambda Exchange Jeff Wereszczynski
- Re: [AMBER] Lambda Exchange Jason Swails
- Re: [AMBER] Is there a way to maintain pdb coordinates into leap? David A Case
- Re: [AMBER] No AMBERHOME/dat/mtkpp folder mmaestre.gate.sinica.edu.tw
- Re: [AMBER] No AMBERHOME/dat/mtkpp folder Jason Swails
- [AMBER] Problem on generating topology file of lithium based electrolyte using GAFF Debashis Kundu
- Re: [AMBER] Is there a way to maintain pdb coordinates into leap? Jonathan Gough
- [AMBER] Torsion Scan Zachary Davis
- Re: [AMBER] Torsion Scan Dwight McGee
Thursday, 9 October 2014
- [AMBER] Error: FFTW configure returned 77 during AMBER 12 installation sunita.tifrh.res.in
- [AMBER] Zinc Paramitarization Patrick Appiah-Kubi
- [AMBER] atom coordinate disagreement with sander TI Hannes Loeffler
- Re: [AMBER] atom coordinate disagreement with sander TI David A Case
- Re: [AMBER] Error: FFTW configure returned 77 during AMBER 12 installation Jason Swails
- Re: [AMBER] Error: FFTW configure returned 77 during AMBER 12 installation sunita.tifrh.res.in
- Re: [AMBER] problems with "Could not find vdW" Investigador Química
- Re: [AMBER] problems with "Could not find vdW" Daniel Roe
- Re: [AMBER] problems with "Could not find vdW" Investigador Química
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand
- Re: [AMBER] atom coordinate disagreement with sander TI Hannes Loeffler
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand
- Re: [AMBER] Zinc Paramitarization Pengfei Li
- [AMBER] Zinc Parameterization Patrick Appiah-Kubi
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand
- [AMBER] cpptraj hbond: query on output George Tzotzos
- Re: [AMBER] cpptraj hbond: query on output Daniel Roe
- [AMBER] force field for lithium ion Evans, Shalton
- Re: [AMBER] force field for lithium ion Mohd Farid Ismail
- Re: [AMBER] cpptraj hbond: query on output George Tzotzos
- Re: [AMBER] cpptraj hbond: query on output Daniel Roe
- [AMBER] Questions about restarting REMD simulations 王漠野
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas
Friday, 10 October 2014
- [AMBER] CUDA test failed Niels Geudens
- [AMBER] crashing multisander with TI/dummy Hannes Loeffler
- Re: [AMBER] Questions about restarting REMD simulations Daniel Roe
- Re: [AMBER] CUDA test failed Jason Swails
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand
- Re: [AMBER] Questions about restarting REMD simulations Jason Swails
- Re: [AMBER] Questions about restarting REMD simulations 王漠野
- Re: [AMBER] Questions about restarting REMD simulations 王漠野
- Re: [AMBER] Questions about restarting REMD simulations Jason Swails
Saturday, 11 October 2014
- [AMBER] Restarting MD production run Soumendranath Bhakat
- Re: [AMBER] Restarting MD production run Daniel Roe
- [AMBER] Forcefield_PTM Sourav Purohit
- Re: [AMBER] Forcefield_PTM Adrian Roitberg
- [AMBER] solvation free energy kirtana S
Sunday, 12 October 2014
- Re: [AMBER] solvation free energy David A Case
- [AMBER] About error of the Pmemd.cuda (14)/ aMD Yeng-Tseng Wang
- Re: [AMBER] About error of the Pmemd.cuda (14)/ aMD Daniel Roe
- [AMBER] dendrimer-query Martiniano Bello Ramirez
- Re: [AMBER] dendrimer-query Daniel Roe
- Re: [AMBER] solvation free energy kirtana S
- Re: [AMBER] solvation free energy David A Case
- [AMBER] Calcium possibly replaced by carbon with MCPB mmaestre.gate.sinica.edu.tw
- [AMBER] why total energy of the system is on the rise in NVE ensemble zhangmk
- Re: [AMBER] why total energy of the system is on the rise in NVE ensemble James Maier
- Re: [AMBER] Forcefield_PTM Ying-Chieh Sun
- [AMBER] DFTB3 in Amber Eric Lang
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas
Monday, 13 October 2014
- [AMBER] Setting exclusions correctly Arun Srikanth
- [AMBER] Problem with lone pair Giachetti Andrea - CERM
- [AMBER] Building Amber 14 for Intel PHIs Baker D.J.
- Re: [AMBER] Forcefield_PTM Sourav Purohit
- Re: [AMBER] Calcium possibly replaced by carbon with MCPB Ken Merz
- Re: [AMBER] DFTB3 in Amber Gustavo Seabra
- Re: [AMBER] Calcium possibly replaced by carbon with MCPB mmaestre.gate.sinica.edu.tw
- Re: [AMBER] Calcium possibly replaced by carbon with MCPB Ken Merz
- Re: [AMBER] Calcium possibly replaced by carbon with MCPB Pengfei Li
- Re: [AMBER] dendrimer-query Vishal Maingi
- [AMBER] Problem installing amber14 肖立
- Re: [AMBER] Building Amber 14 for Intel PHIs Ross Walker
- Re: [AMBER] Calcium possibly replaced by carbon with MCPB FyD
- [AMBER] ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 46946 0 Hirdesh Kumar
- Re: [AMBER] ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 46946 0 David A Case
- Re: [AMBER] ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 46946 0 Hirdesh Kumar
- [AMBER] How to install sander.MPI? Zhong, Roger
- [AMBER] Amber 14 compile error 汪盛
- Re: [AMBER] Calcium possibly replaced by carbon with MCPB mmaestre.gate.sinica.edu.tw
- Re: [AMBER] Calcium possibly replaced by carbon with MCPB mmaestre.gate.sinica.edu.tw
- Re: [AMBER] Calcium possibly replaced by carbon with MCPB mmaestre.gate.sinica.edu.tw
- Re: [AMBER] ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 46946 0 David A Case
- Re: [AMBER] How to install sander.MPI? David A Case
- Re: [AMBER] Amber 14 compile error David A Case
- Re: [AMBER] solvation free energy kirtana S
- Re: [AMBER] solvation free energy kirtana S
Tuesday, 14 October 2014
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas
- Re: [AMBER] Building Amber 14 for Intel PHIs Baker D.J.
- [AMBER] principal axes cpptraj Asmita Gupta
- Re: [AMBER] solvation free energy David A Case
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas
- Re: [AMBER] Calcium possibly replaced by carbon with MCPB Pengfei Li
- Re: [AMBER] Calcium possibly replaced by carbon with MCPB Pengfei Li
- [AMBER] Errors while attempting .prmtop file production Evans, Shalton
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand
- [AMBER] GIST dx files Gard Nelson
- Re: [AMBER] Errors while attempting .prmtop file production David A Case
- Re: [AMBER] GIST dx files Jonathan Gough
- Re: [AMBER] GIST dx files Nguyen, Crystal
- Re: [AMBER] principal axes cpptraj Daniel Roe
- Re: [AMBER] dendrimer-query Daniel Roe
- [AMBER] Loss of secondary structure in GB simulations Nihal Korkmaz
- Re: [AMBER] Setting exclusions correctly Jason Swails
- Re: [AMBER] Setting exclusions correctly Daniel Roe
- Re: [AMBER] Problem with lone pair Jason Swails
- Re: [AMBER] Calcium possibly replaced by carbon with MCPB mmaestre.gate.sinica.edu.tw
- Re: [AMBER] GIST dx files Gard Nelson
- Re: [AMBER] Setting exclusions correctly Arun Srikanth
- Re: [AMBER] why total energy of the system is on the rise in NVE ensemble Hector A. Baldoni
- Re: [AMBER] Loss of secondary structure in GB simulations Carlos Simmerling
- [AMBER] Amber for beginner Suraya Abdul Sani
- Re: [AMBER] Amber for beginner Jonathan Gough
- Re: [AMBER] Calcium possibly replaced by carbon with MCPB mmaestre.gate.sinica.edu.tw
- Re: [AMBER] Loss of secondary structure in GB simulations Nihal Korkmaz
- Re: [AMBER] Amber for beginner Raman Parkesh
- [AMBER] How can I do MD simulation of a protein-ligand complex where the ligand is covalently attached to the protein Bikash Ranjan Sahoo
- Re: [AMBER] Calcium possibly replaced by carbon with MCPB Pengfei Li
- Re: [AMBER] QM/MM in amber, PME when qm_theory='extern' Andreas Goetz
- Re: [AMBER] Loss of secondary structure in GB simulations Hai Nguyen
Wednesday, 15 October 2014
- Re: [AMBER] why total energy of the system is on the rise in NVE ensemble David A Case
- [AMBER] How can I do MD simulation of a protein-ligand complex where the ligand is covalently attached to the protein Bikash Ranjan Sahoo
- [AMBER] TI and FEW sabine.ruppel.boehringer-ingelheim.com
- Re: [AMBER] Loss of secondary structure in GB simulations Nihal Korkmaz
- [AMBER] Setting exclusions - am i overcounting ? Arun Srikanth
- Re: [AMBER] Loss of secondary structure in GB simulations Nhai
- Re: [AMBER] Setting exclusions - am i overcounting ? Daniel Roe
- Re: [AMBER] Setting exclusions - am i overcounting ? Arun Srikanth
- [AMBER] How can I do MD simulation of a protein-ligand complex where the ligand is covalently attached to the protein Bikash Ranjan Sahoo
- Re: [AMBER] Setting exclusions - am i overcounting ? Jason Swails
- Re: [AMBER] TI and FEW David A Case
- Re: [AMBER] Setting exclusions - am i overcounting ?-Last question Arun Srikanth
- Re: [AMBER] Setting exclusions correctly Jason Swails
- Re: [AMBER] Setting exclusions - am i overcounting ?-Last question Jason Swails
- Re: [AMBER] Setting exclusions - am i overcounting ?-Last question Arun Srikanth
- [AMBER] Small NAB program: Not getting desired output Himanshu Joshi
- Re: [AMBER] Small NAB program: Not getting desired output Himanshu Joshi
Thursday, 16 October 2014
- Re: [AMBER] Small NAB program: Not getting desired output David A Case
- [AMBER] amber-Gaussian 王珍
- Re: [AMBER] TI and FEW sabine.ruppel.boehringer-ingelheim.com
- Re: [AMBER] TI and FEW David A Case
- [AMBER] Plotting Issue Soumendranath Bhakat
- Re: [AMBER] Plotting Issue Jason Swails
- Re: [AMBER] dendrimer-query Vishal Maingi
- [AMBER] Problem with input coordinates file Francesco Gentile
- [AMBER] Loadpdb in Tleap takes forever Ahmed Ayoub
- [AMBER] install error after updates Nihal Korkmaz
- Re: [AMBER] install error after updates Daniel Roe
- Re: [AMBER] Problem with input coordinates file Daniel Roe
- Re: [AMBER] Loadpdb in Tleap takes forever Daniel Roe
- Re: [AMBER] Problem with input coordinates file Francesco Gentile
- Re: [AMBER] Problem with input coordinates file Daniel Roe
- [AMBER] source leaprc.constph error jinfeng liu
- Re: [AMBER] source leaprc.constph error Jason Swails
- Re: [AMBER] source leaprc.constph error jinfeng liu
- Re: [AMBER] source leaprc.constph error Jason Swails
- Re: [AMBER] source leaprc.constph error jinfeng liu
- [AMBER] Which GPU is recommended? xueqiaoup.gmail.com
Friday, 17 October 2014
- Re: [AMBER] Need help for retrained MD (Daniel Roe) Sudhanshu Shanker
- Re: [AMBER] Small NAB program: Not getting desired output Himanshu Joshi
- Re: [AMBER] Small NAB program: Not getting desired output David A Case
- Re: [AMBER] Need help for retrained MD (Daniel Roe) Daniel Roe
- Re: [AMBER] Which GPU is recommended? Ross Walker
- Re: [AMBER] Problem with input coordinates file Daniel Roe
- [AMBER] Jarzynski SMD George Tzotzos
- Re: [AMBER] Problem with input coordinates file Francesco Gentile
- Re: [AMBER] Jarzynski SMD Jason Swails
Saturday, 18 October 2014
- [AMBER] thanks zayan alhalabi
- [AMBER] Regarding impropers from parmed.py and guessing from bond topology Arun Srikanth
- Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Daniel Roe
- Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Jason Swails
- Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology David A Case
- Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Arun Srikanth
- Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Jason Swails
Sunday, 19 October 2014
- [AMBER] solvation of a pdb file Robin Jain
- Re: [AMBER] solvation of a pdb file David A Case
- [AMBER] Fwd: Desmond trajectory use with AMBER D.A. Ragland
- [AMBER] Heating Problem jinfeng liu
- Re: [AMBER] Fwd: Desmond trajectory use with AMBER Daniel Roe
- Re: [AMBER] Desmond trajectory use with AMBER D.A. Ragland
- Re: [AMBER] Heating Problem Daniel Roe
- Re: [AMBER] Desmond trajectory use with AMBER Daniel Roe
- Re: [AMBER] Desmond trajectory use with AMBER D.A. Ragland
- Re: [AMBER] Desmond trajectory use with AMBER Daniel Roe
- [AMBER] Parameters for Boron atom 王璇
- Re: [AMBER] Fwd: Desmond trajectory use with AMBER jojartb.jgypk.u-szeged.hu
- Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Arun Srikanth
- Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Jason Swails
- Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Arun Srikanth
- Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Jason Swails
- Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Arun Srikanth
Monday, 20 October 2014
- [AMBER] Complex MD with protein ligand covalent bond Bikash Ranjan Sahoo
- [AMBER] MMGBSA & igb 8 jojartb.jgypk.u-szeged.hu
- [AMBER] Problem regarding Chamber Shubhadip Das
- Re: [AMBER] Parameters for Boron atom David A Case
- Re: [AMBER] Complex MD with protein ligand covalent bond David A Case
- Re: [AMBER] TI and FEW Nadine Homeyer
- Re: [AMBER] Problem regarding Chamber Jason Swails
- Re: [AMBER] MMGBSA & igb 8 Jason Swails
- Re: [AMBER] MMGBSA & igb 8 Carlos Simmerling
- [AMBER] Carboxyl and Carboxylate groups with GLYCAM sa
- [AMBER] How can I get amber know calcium jinfeng liu
- Re: [AMBER] How can I get amber know calcium Sajeewa Pemasinghe
- Re: [AMBER] How can I get amber know calcium Jason Swails
- Re: [AMBER] How can I get amber know calcium jinfeng liu
- Re: [AMBER] How can I get amber know calcium Chinthaka Ratnaweera
- Re: [AMBER] How can I get amber know calcium Pengfei Li
- Re: [AMBER] How can I get amber know calcium Chinthaka Ratnaweera
- Re: [AMBER] How can I get amber know calcium Pengfei Li
- Re: [AMBER] How can I get amber know calcium Ken Merz
- Re: [AMBER] How can I get amber know calcium Chinthaka Ratnaweera
- Re: [AMBER] How can I get amber know calcium Pengfei Li
- Re: [AMBER] How can I get amber know calcium mmaestre.gate.sinica.edu.tw
Tuesday, 21 October 2014
- [AMBER] Chains missing during the simulation Harshavardhan Khare
- Re: [AMBER] Chains missing during the simulation Jason Swails
- [AMBER] Forcefield_PTM Sourav Purohit
- Re: [AMBER] Forcefield_PTM Jason Swails
- [AMBER] Cpptraj: Move origin to specific coordinates Waldner, Birgit
- Re: [AMBER] Forcefield_PTM David A Case
- Re: [AMBER] Cpptraj: Move origin to specific coordinates Daniel Roe
- Re: [AMBER] Forcefield_PTM Sourav Purohit
- Re: [AMBER] Cpptraj: Move origin to specific coordinates Waldner, Birgit
- Re: [AMBER] Cpptraj: Move origin to specific coordinates Daniel Roe
- Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM Lachele Foley
- Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM sa
- Re: [AMBER] Problem with input coordinates file Francesco Gentile
- Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM Lachele Foley
- Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM sa
- Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM Lachele Foley
- Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM sa
- [AMBER] BSUB on LSF cluster D.A. Ragland
- Re: [AMBER] BSUB on LSF cluster Jason Swails
- Re: [AMBER] BSUB on LSF cluster D.A. Ragland
- Re: [AMBER] BSUB on LSF cluster D.A. Ragland
- Re: [AMBER] BSUB on LSF cluster Jason Swails
Wednesday, 22 October 2014
- [AMBER] Info About GPU and PMEMD versions Lorenzo Gontrani
- [AMBER] ANTECHAMBER tutorial Sourav Purohit
- Re: [AMBER] Which GPU is recommended? Alexander Metz
- Re: [AMBER] Chains missing during the simulation Harshavardhan Khare
- Re: [AMBER] Which GPU is recommended? Jason Swails
- Re: [AMBER] ANTECHAMBER tutorial Jason Swails
- Re: [AMBER] ANTECHAMBER tutorial Sourav Purohit
- Re: [AMBER] Info About GPU and PMEMD versions Jason Swails
- Re: [AMBER] Info About GPU and PMEMD versions Ross Walker
- [AMBER] Forcefield for RNA Asfa Ali
Thursday, 23 October 2014
- Re: [AMBER] Problem regarding Chamber Jason Swails
- Re: [AMBER] Forcefield for RNA Jiri Sponer
- Re: [AMBER] Forcefield for RNA Jiri Sponer
- [AMBER] peptideligandParameters zayan alhalabi
- Re: [AMBER] Forcefield for RNA Ilyas Yildirim
- Re: [AMBER] Forcefield for RNA Jason Swails
- Re: [AMBER] Forcefield for RNA Asfa Ali
- Re: [AMBER] Forcefield for RNA David A Case
- [AMBER] Number of water hits and density Suhaib Shekfeh
- Re: [AMBER] Number of water hits and density Carlos Simmerling
- Re: [AMBER] Number of water hits and density Thomas Cheatham
- Re: [AMBER] Forcefield for RNA pavel.banas.upol.cz
- Re: [AMBER] Forcefield for RNA Jiri Sponer
- Re: [AMBER] Forcefield for RNA koushik
- Re: [AMBER] Forcefield for RNA koushik
- Re: [AMBER] Forcefield for RNA Jiri Sponer
- [AMBER] MMGBSA doesn't finish Bernhard Poll
Friday, 24 October 2014
- [AMBER] AMBER GAUSSIAN QM/MM Ayesha Fatima
- Re: [AMBER] AMBER GAUSSIAN QM/MM Marc van der Kamp
- [AMBER] Heme Parameters 杨川
- Re: [AMBER] AMBER GAUSSIAN QM/MM Ayesha Fatima
- Re: [AMBER] Heme Parameters Jason Swails
- Re: [AMBER] MMGBSA doesn't finish Jason Swails
- Re: [AMBER] Heme Parameters David A Case
- Re: [AMBER] Forcefield for RNA Asfa Ali
- Re: [AMBER] peptideligandParameters Jason Swails
- Re: [AMBER] Forcefield for RNA Jason Swails
- Re: [AMBER] Problem regarding Chamber Jason Swails
- Re: [AMBER] peptideligandParameters FyD
Saturday, 25 October 2014
- Re: [AMBER] Forcefield for RNA Asfa Ali
- [AMBER] PDB to P2N conversion Sylvester Tumusiime
- [AMBER] problem with extra-point Emilio Angelina
- Re: [AMBER] PDB to P2N conversion ABEL Stephane 175950
- Re: [AMBER] problem with extra-point David A Case
- [AMBER] Temperature not correctly maintained using AMBER14 Gonzalo Jimenez
- Re: [AMBER] Temperature not correctly maintained using AMBER14 Ross Walker
- Re: [AMBER] Temperature not correctly maintained using AMBER14 Gonzalo Jimenez
Sunday, 26 October 2014
- Re: [AMBER] Number of water hits and density Suhaib Shekfeh
- Re: [AMBER] Temperature not correctly maintained using AMBER14 Ross Walker
- Re: [AMBER] Temperature not correctly maintained using AMBER14 Gonzalo Jimenez
- Re: [AMBER] Temperature not correctly maintained using AMBER14 Ross Walker
- [AMBER] Problem regarding Chamber Shubhadip Das
Monday, 27 October 2014
- [AMBER] MMPBSA Error: PB Bomb in pb_atmlist(): maxnba too short MOHD HOMAIDUR RAHMAN
- Re: [AMBER] MMPBSA Error: PB Bomb in pb_atmlist(): maxnba too short Jason Swails
- [AMBER] Problem regarding Chamber and psf file Caitlin Scott
- Re: [AMBER] Problem regarding Chamber and psf file Jason Swails
- Re: [AMBER] Problem regarding Chamber Jason Swails
- [AMBER] Running G03 Brittany Boykin
- Re: [AMBER] Running G03 Kshatresh Dutta Dubey
- [AMBER] GPU enabled Hardware specification M. Reza Ganjalikhany
- Re: [AMBER] GPU enabled Hardware specification Scott Le Grand
- [AMBER] Regarding Protein-ligand MD Bikash Ranjan Sahoo
- Re: [AMBER] Regarding Protein-ligand MD Robin Betz
- Re: [AMBER] Regarding Protein-ligand MD Bikash Ranjan Sahoo
- Re: [AMBER] Running G03 FyD
Tuesday, 28 October 2014
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas
- Re: [AMBER] Regarding Protein-ligand MD FyD
- Re: [AMBER] GPU enabled Hardware specification M. Reza Ganjalikhany
- Re: [AMBER] GPU enabled Hardware specification Jonathan Gough
- Re: [AMBER] GPU enabled Hardware specification Jonathan Gough
- Re: [AMBER] GPU enabled Hardware specification Ross Walker
- [AMBER] loading force field ff14SB Vlad Cojocaru
- Re: [AMBER] loading force field ff14SB Jason Swails
- Re: [AMBER] loading force field ff14SB Christina Bergonzo
- Re: [AMBER] loading force field ff14SB Vlad Cojocaru
- Re: [AMBER] loading force field ff14SB Jiri Sponer
- Re: [AMBER] GPU enabled Hardware specification M. Reza Ganjalikhany
- Re: [AMBER] GPU enabled Hardware specification Scott Le Grand
- Re: [AMBER] GPU enabled Hardware specification Ross Walker
- [AMBER] Problem about "Too many dipole_dipole interactions for allocated" when heat Ya Gao
- [AMBER] Entropy calculation asdda asa
- Re: [AMBER] How do MCPB make sidechain.bcl? Saeed Nasiri
- [AMBER] Problem about "Too many dipole_dipole interactions for allocated" in heat simulation Tong Zhu
Wednesday, 29 October 2014
- [AMBER] problem in DNA-ligand trajectory Mina Madah
- Re: [AMBER] Problem about "Too many dipole_dipole interactions for allocated" when heat David A Case
- Re: [AMBER] Problem about "Too many dipole_dipole interactions for allocated" when heat Lorenzo Gontrani
- Re: [AMBER] Problem about "Too many dipole_dipole interactions for allocated" when heat Ya Gao
- [AMBER] Imaging Sylvester Tumusiime
- Re: [AMBER] Imaging Daniel Roe
- [AMBER] restart file position Fabian Glaser
- Re: [AMBER] Imaging Sylvester Tumusiime
- Re: [AMBER] Imaging Daniel Roe
- Re: [AMBER] Imaging Sylvester Tumusiime
- Re: [AMBER] Imaging Sylvester Tumusiime
- Re: [AMBER] restart file position Jason Swails
- [AMBER] Implementing parameterized heme? Kevin Murphy
- Re: [AMBER] problem in DNA-ligand trajectory Jason Swails
- Re: [AMBER] Entropy calculation Jason Swails
- Re: [AMBER] Implementing parameterized heme? Pengfei Li
- Re: [AMBER] Implementing parameterized heme? Pengfei Li
- Re: [AMBER] How do MCPB make sidechain.bcl? Pengfei Li
- Re: [AMBER] Imaging Daniel Roe
- Re: [AMBER] Imaging Sylvester Tumusiime
- Re: [AMBER] Implementing parameterized heme? Yarrow Madrona
- Re: [AMBER] Implementing parameterized heme? Yarrow Madrona
- Re: [AMBER] Entropy calculation asdda asa
Thursday, 30 October 2014
- [AMBER] using multiple force fields in a simulation Bhushan
- Re: [AMBER] using multiple force fields in a simulation Hannes Loeffler
- [AMBER] visualize CPPTRAJ clculated modes Vlad Cojocaru
- Re: [AMBER] visualize CPPTRAJ clculated modes Jason Swails
- Re: [AMBER] visualize CPPTRAJ clculated modes Vlad Cojocaru
- Re: [AMBER] visualize CPPTRAJ clculated modes Daniel Roe
- Re: [AMBER] using multiple force fields in a simulation Carlos Simmerling
- [AMBER] Multiple timecorr commands in one cpptraj script Eugene Yedvabny
- [AMBER] 3D Histogram in cpptraj CHAMI F.
- Re: [AMBER] 3D Histogram in cpptraj Asaminew Haile
- Re: [AMBER] 3D Histogram in cpptraj CHAMI F.
- Re: [AMBER] Multiple timecorr commands in one cpptraj script George M Giambasu
- Re: [AMBER] Implementing parameterized heme? Pengfei Li
- Re: [AMBER] Implementing parameterized heme? Pengfei Li
- Re: [AMBER] Imaging Sylvester Tumusiime
- Re: [AMBER] Imaging Thomas Cheatham
- Re: [AMBER] Imaging Daniel Roe
- Re: [AMBER] Imaging Sylvester Tumusiime
Friday, 31 October 2014
- [AMBER] pyroglutamic acid or 5-oxoproline Yves Boulard
- [AMBER] About geometry of FAD in the F-90 project of http://q4md-forcefieldtools.org/ Emilio Lence
- [AMBER] Looking force field for beta-peptide MOHD HOMAIDUR RAHMAN
- Re: [AMBER] Problem regarding Chamber and psf file Caitlin Scott
- Re: [AMBER] Problem regarding Chamber and psf file Jason Swails
- Re: [AMBER] 3D Histogram in cpptraj Daniel Roe
- Re: [AMBER] Looking force field for beta-peptide David A Case
- Re: [AMBER] Problem regarding Chamber and psf file Pete Kekenes-Huskey

Last message date: Fri Oct 31 2014 - 14:00:02 PDT
Archived on: Fri Nov 15 2024 - 05:55:05 PST

Amber Archive Oct 2014 by date