Amber Archive Sep 2020: by date

Monday, 31 August 2020
- [AMBER] How to use the ntb options in amber-cuda-version neildancer.sina.com
Tuesday, 1 September 2020
- Re: [AMBER] Attention: All CPPTRAJ Questions Gustaf Olsson
- Re: [AMBER] How to use the ntb options in amber-cuda-version David Cerutti
- Re: [AMBER] How to use the ntb options in amber-cuda-version neildancer.sina.com
- [AMBER] Enquiry Kehinde Idowu
- Re: [AMBER] Enquiry Bill Ross
- [AMBER] Amber 18 generates error: an illegal memory access was encountered launching kernel kNLSkinTest Lucas, Xavier
- Re: [AMBER] Enquiry Kehinde Idowu
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Matias Machado
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Charo del Genio
- [AMBER] Questions on deriving charges for aromatic compounds using The RESP Method Lucas Bandeira
- [AMBER] Generating topology using tleap Lucas Bandeira
- [AMBER] Two problems about Amber's TI totorial ecnu_wangbo
- Re: [AMBER] Enquiry Gustaf Olsson
- Re: [AMBER] Generating topology using tleap Gustaf Olsson
Wednesday, 2 September 2020
- [AMBER] MCPB parametrization for an RNA systems Claire Claire
- [AMBER] best way to umbrella-sample a pseudo-dihedral angle Collective Variable Akshay Prabhakant
- Re: [AMBER] best way to umbrella-sample a pseudo-dihedral angle Collective Variable Bill Ross
- [AMBER] [MicrosoftExchange329e71ec88ae4615bbc36ab6ce41109e@rutgegetting a nucleic acid helix structure David A Case
- Re: [AMBER] best way to umbrella-sample a pseudo-dihedral angle Collective Variable David A Case
- Re: [AMBER] Questions on deriving charges for aromatic compounds using The RESP Method David A Case
- [AMBER] Fw: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Esposito Carmen
- Re: [AMBER] best way to umbrella-sample a pseudo-dihedral angle Collective Variable Kellon Belfon
- Re: [AMBER] [MicrosoftExchange329e71ec88ae4615bbc36ab6ce41109e@rutgegetting a nucleic acid helix structure aishen
- [AMBER] umbrella protein-protein Fabian Glaser
- Re: [AMBER] Questions on deriving charges for aromatic compounds using The RESP Method Lucas Bandeira
- [AMBER] cPHMD: how to define residues with two pkas Kolattukudy P. Santo
- Re: [AMBER] cPHMD: how to define residues with two pkas Cruzeiro,Vinicius Wilian D
Thursday, 3 September 2020
- [AMBER] 30 Series GPUs from Nvidia Homeo Morphism
- [AMBER] MCPB with OPC water? Gustavo Seabra
- Re: [AMBER] executable names from nab David A Case
- Re: [AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane
- Re: [AMBER] executable names from nab aishen
- Re: [AMBER] best way to umbrella-sample a pseudo-dihedral angle Collective Variable Akshay Prabhakant
- [AMBER] Cpptraj pucker amplitude units? Kenneth Huang
- Re: [AMBER] 30 Series GPUs from Nvidia Hashemi, Mohtadin
- Re: [AMBER] Fw: covalent molecule and modified residue parameters David A Case
- Re: [AMBER] Fw: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion David A Case
- [AMBER] Molecular creations rather than annihilations in AMBER18/20 Debarati DasGupta
- [AMBER] Molecular creations rather than annihilations in AMBER18/20 Debarati DasGupta
- [AMBER] | ERROR: I could not find enough velocities in 1346.rst7 Lod King
- Re: [AMBER] | ERROR: I could not find enough velocities in 1346.rst7 Bill Ross
- Re: [AMBER] | ERROR: I could not find enough velocities in 1346.rst7 Lod King
- Re: [AMBER] | ERROR: I could not find enough velocities in 1346.rst7 Bill Ross
Friday, 4 September 2020
- Re: [AMBER] Fw: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Charo del Genio
- Re: [AMBER] Fw: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Esposito Carmen
- Re: [AMBER] Amber 18 generates error: an illegal memory access was encountered launching kernel kNLSkinTest David A Case
- Re: [AMBER] | ERROR: I could not find enough velocities in 1346.rst7 Daniel Roe
- Re: [AMBER] Cpptraj pucker amplitude units? Daniel Roe
- Re: [AMBER] "After the fact" lifetime analysis with CPPTRAJ Daniel Roe
- Re: [AMBER] How to select groups for energy calculations-CPPtraj Daniel Roe
- Re: [AMBER] Generating topology using tleap Lucas Bandeira
- Re: [AMBER] How to use the ntb options in amber-cuda-version Daniel Roe
- Re: [AMBER] Stripping Protocol in Cpptraj Daniel Roe
- Re: [AMBER] Confusion regarding Center of mass coordinates for protein, with CPPTRAJ Daniel Roe
- Re: [AMBER] Change covar matrix precision when crdaction is used Daniel Roe
- Re: [AMBER] Unable to complete heating stage Daniel Roe
- Re: [AMBER] Stripping Protocol in Cpptraj An Ta
- Re: [AMBER] Stripping Protocol in Cpptraj Daniel Roe
- [AMBER] Cyclic peptides in Amber? Alexander Izvorski
Saturday, 5 September 2020
- [AMBER] constant pH MD in explicit solvent SATYAJIT KHATUA
- Re: [AMBER] Cyclic peptides in Amber? Bill Ross
- [AMBER] RMSD do not increase with the increase of temperature ali akbar
- Re: [AMBER] RMSD do not increase with the increase of temperature Bill Ross
- Re: [AMBER] Cyclic peptides in Amber? Alexander Izvorski
- Re: [AMBER] Cyclic peptides in Amber? Bill Ross
- Re: [AMBER] Cyclic peptides in Amber? Bill Ross
- Re: [AMBER] constant pH MD in explicit solvent Cruzeiro,Vinicius Wilian D
- Re: [AMBER] Cyclic peptides in Amber? David A Case
Sunday, 6 September 2020
- Re: [AMBER] How to use the ntb options in amber-cuda-version neildancer.sina.com
- Re: [AMBER] Cyclic peptides in Amber? Alexander Izvorski
- [AMBER] finding number of atoms within a radius Saikat Pal
Monday, 7 September 2020
- Re: [AMBER] finding number of atoms within a radius Elvis Martis
- Re: [AMBER] finding number of atoms within a radius Saikat Pal
- [AMBER] Parametrization of GTP and terminal phosphate of DNA Jenny 148
- [AMBER] Simulation of 10 ns DNA - ligand intercalation Erdem Yeler
- [AMBER] Just for info aishen
- Re: [AMBER] Just for info Bill Ross
- Re: [AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane
- Re: [AMBER] Parametrization of GTP and terminal phosphate of DNA David A Case
- Re: [AMBER] Simulation of 10 ns DNA - ligand intercalation David A Case
- Re: [AMBER] Just for info David A Case
- Re: [AMBER] Fw: covalent molecule and modified residue parameters David A Case
- Re: [AMBER] Simulation of 10 ns DNA - ligand intercalation Erdem Yeler
- Re: [AMBER] Parametrization of GTP and terminal phosphate of DNA Jenny 148
- [AMBER] Cluster representation over trajectory Hector A. Baldoni
- Re: [AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane
- Re: [AMBER] Cluster representation over trajectory Hector A. Baldoni
- Re: [AMBER] cPHMD: how to define residues with two pkas Kolattukudy P. Santo
- Re: [AMBER] Just for info aishen
- Re: [AMBER] Fw: covalent molecule and modified residue parameters David A Case
- Re: [AMBER] Parametrization of GTP and terminal phosphate of DNA Jenny 148
- [AMBER] Combining repeated MD trajectories Nada Afiva
- [AMBER] AmberHub down ? Setyanto Md
- Re: [AMBER] AmberHub down ? Rodrigo Galindo-Murillo
- Re: [AMBER] AmberHub down ? Setyanto Md
- Re: [AMBER] Combining repeated MD trajectories Song, Lin
- Re: [AMBER] Combining repeated MD trajectories Nada Afiva
- Re: [AMBER] Combining repeated MD trajectories Rodrigo Galindo-Murillo
- [AMBER] free binding energy Kehinde Idowu
- Re: [AMBER] Combining repeated MD trajectories Nada Afiva
Tuesday, 8 September 2020
- Re: [AMBER] free binding energy Song, Lin
- Re: [AMBER] Combining repeated MD trajectories Clorice Reinhardt
- Re: [AMBER] Combining repeated MD trajectories Setyanto Md
- [AMBER] "nan" appeared in mmpbsa result Xinye Wang
- Re: [AMBER] Combining repeated MD trajectories Nada Afiva
- Re: [AMBER] MCPB with OPC water? Gustavo Seabra
- Re: [AMBER] MCPB with OPC water? David Cerutti
- Re: [AMBER] MCPB with OPC water? Casalini Tommaso
- Re: [AMBER] MCPB with OPC water? Gustavo Seabra
- [AMBER] Strange RMSD tower appearing in simulation Jorge da Rocha
- Re: [AMBER] Strange RMSD tower appearing in simulation Carlos Simmerling
- Re: [AMBER] Strange RMSD tower appearing in simulation David Cerutti
- Re: [AMBER] Cartesian restraints on Production phase David A Case
- Re: [AMBER] Strange RMSD tower appearing in simulation David A Case
- [AMBER] OE Tool kit Debarati DasGupta
- Re: [AMBER] "nan" appeared in mmpbsa result Ray Luo
- [AMBER] protein-protein interaction plot Kehinde Idowu
- [AMBER] antechamber & parmck2 Lod King
- [AMBER] Adding ions at a particular position Athena N
Wednesday, 9 September 2020
- Re: [AMBER] Adding ions at a particular position Gustaf Olsson
- Re: [AMBER] antechamber & parmck2 Gustaf Olsson
- Re: [AMBER] Adding ions at a particular position Dr. Anselm Horn
- Re: [AMBER] Strange RMSD tower appearing in simulation Dr. Anselm Horn
- [AMBER] The status of GAFF2 Gustaf Olsson
- Re: [AMBER] OE Tool kit Raman Preet Singh
- Re: [AMBER] Strange RMSD tower appearing in simulation Jorge da Rocha
- [AMBER] PLUMED masterclass David A Case
- Re: [AMBER] error tleap Gustaf Olsson
- Re: [AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane
- [AMBER] OE tools help Debarati DasGupta
- Re: [AMBER] antechamber & parmck2 Lod King
- Re: [AMBER] Strange RMSD tower appearing in simulation David Cerutti
- Re: [AMBER] AMBER Digest, Vol 3114, Issue 1 SATYAJIT KHATUA
- Re: [AMBER] error tleap MYRIAN TORRES RICO
- [AMBER] Growing of small molecules instead of annihilation of molecules in amber TI simulations Debarati DasGupta
- [AMBER] Normal Model Analysis with AmberTools20 Harley Wilson
- Re: [AMBER] antechamber & parmck2 Gustaf Olsson
Thursday, 10 September 2020
- Re: [AMBER] antechamber & parmck2 Lod King
- Re: [AMBER] error tleap Gustaf Olsson
- Re: [AMBER] antechamber & parmck2 Gustaf Olsson
- Re: [AMBER] OE tools help Raman Preet Singh
- Re: [AMBER] error tleap MYRIAN TORRES RICO
- Re: [AMBER] OE tools help Raman Preet Singh
- Re: [AMBER] azobenzene atoms name in amber format Aashish Bhatt
- Re: [AMBER] error tleap Gustaf Olsson
- [AMBER] SHAKEH hydrogen clusters Pietro Aronica
- [AMBER] problem with cpptraj Marko Sever
- Re: [AMBER] problem with cpptraj Daniel Roe
- Re: [AMBER] Growing of small molecules instead of annihilation of molecules in amber TI simulations David A Case
- Re: [AMBER] problem with cpptraj Marko Sever
- Re: [AMBER] Normal Model Analysis with AmberTools20 David A Case
- [AMBER] Regarding help in installation (LINUX ubuntu) swapnil singh
- Re: [AMBER] problem with cpptraj Daniel Roe
- Re: [AMBER] SHAKEH hydrogen clusters David A Case
- Re: [AMBER] Regarding help in installation (LINUX ubuntu) David A Case
- Re: [AMBER] Refitting charges with MCPB destabilizes the active site Pengfei Li
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Pengfei Li
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Pengfei Li
- Re: [AMBER] MCPB parametrization for an RNA systems Pengfei Li
- Re: [AMBER] MCPB with OPC water? Pengfei Li
- Re: [AMBER] SHAKEH hydrogen clusters pietroa.bii.a-star.edu.sg
- [AMBER] Visualizing the system trajectory from .nc file Jatin Kashyap
- Re: [AMBER] Visualizing the system trajectory from .nc file Emmett Leddin
Friday, 11 September 2020
- Re: [AMBER] Regarding help in installation (LINUX ubuntu) Raman Preet Singh
- Re: [AMBER] Regarding help in installation (LINUX ubuntu) aishen
- [AMBER] Dextrins zmatovic.kg.ac.rs
- Re: [AMBER] error tleap MYRIAN TORRES RICO
- [AMBER] Dynamic cross correlation between the center of mass of two groups of atoms Jorden Cabal
- Re: [AMBER] MCPB with OPC water? Gustavo Seabra
- [AMBER] AQUA-DUCT Webinar 23rd September 2020 Maria Bzówka
- [AMBER] Fwd: azobenzene atoms name in amber format Aashish Bhatt
- Re: [AMBER] Fwd: azobenzene atoms name in amber format David A Case
- Re: [AMBER] SHAKEH hydrogen clusters David A Case
- Re: [AMBER] Dynamic cross correlation between the center of mass of two groups of atoms David A Case
- Re: [AMBER] SHAKEH hydrogen clusters pietroa.bii.a-star.edu.sg
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Vaibhav Dixit
Saturday, 12 September 2020
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Vaibhav Dixit
- Re: [AMBER] Growing of small molecules instead of annihilation of molecules in amber TI simulations Debarati DasGupta
Monday, 14 September 2020
- [AMBER] constant pH MD in explicit solvent SATYAJIT KHATUA
- [AMBER] pymsmt.exp.pymsmtError: MOL is required in naa_mol2files but not provided. CHENTOUF Sara
- Re: [AMBER] constant pH MD in explicit solvent Cruzeiro,Vinicius Wilian D
- Re: [AMBER] Visualizing the system trajectory from .nc file Jatin Kashyap
Tuesday, 15 September 2020
- [AMBER] Of possible interest: Chem Faiss Bill Ross
- Re: [AMBER] error tleap Gustaf Olsson
- [AMBER] preparing parameter files for a ligand Siavoush Dastmalchi
- [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations Vaibhav Dixit
Wednesday, 16 September 2020
- Re: [AMBER] error tleap MYRIAN TORRES RICO
- Re: [AMBER] error tleap Gustaf Olsson
- [AMBER] Is it possible to run QM/MM-PIMD simulations with sander? proszx
- Re: [AMBER] preparing parameter files for a ligand David A Case
- [AMBER] adding lysyl-phosphatidylglycerol and cardiolipin Chetna Tyagi
- Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations David A Case
- Re: [AMBER] preparing parameter files for a ligand Siavoush Dastmalchi
- [AMBER] Query on nucleic acid force fields Jenny 148
- [AMBER] Generate deleted .rst file from coordinates? Alysia Mandato
- [AMBER] Advice on calculating binding energies of enantiomers Billiot, Eugene
- Re: [AMBER] Generate deleted .rst file from coordinates? Daniel Roe
- Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations Vaibhav Dixit
- [AMBER] Tleap creates only one residue Farkhad Maksudov
- Re: [AMBER] Tleap creates only one residue Bill Ross
- [AMBER] constant pH error Kolattukudy P. Santo
- Re: [AMBER] Query on nucleic acid force fields David Cerutti
- Re: [AMBER] Query on nucleic acid force fields Jenny 148
- Re: [AMBER] Query on nucleic acid force fields David Cerutti
Thursday, 17 September 2020
- Re: [AMBER] Query on nucleic acid force fields Jiri Sponer
- Re: [AMBER] Query on nucleic acid force fields Jenny 148
- Re: [AMBER] Query on nucleic acid force fields Jiri Sponer
- [AMBER] BR atom moved out Nisha Amarnath Jonniya
- Re: [AMBER] Tleap creates only one residue David A Case
- Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations David A Case
- Re: [AMBER] SHAKEH hydrogen clusters David A Case
- Re: [AMBER] Generate deleted .rst file from coordinates? Alysia Mandato
- Re: [AMBER] constant pH error Cruzeiro,Vinicius Wilian D
- Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations Vaibhav Dixit
- Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations Adrian Roitberg
- Re: [AMBER] constant pH error Kolattukudy P. Santo
- Re: [AMBER] Tleap creates only one residue Farkhad Maksudov
- [AMBER] Perturbing charges Delwakkada Liyanage, Senal Dinuka
- Re: [AMBER] Perturbing charges David A Case
- [AMBER] RMSD of nucleic acid bases Sruthi Sudhakar
- Re: [AMBER] RMSD of nucleic acid bases Saikat Pal
Friday, 18 September 2020
- Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations Vaibhav Dixit
- [AMBER] antechamber problem with negatively charged nitrogen Giorgos Lambrinidis
- Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations David A Case
- Re: [AMBER] Perturbing charges Delwakkada Liyanage, Senal Dinuka
- [AMBER] constant pH MD in explicit solvent SATYAJIT KHATUA
- [AMBER] ddikick.x error during Fe3+ ion parameter derivation using Gamess gagandeep singh
- [AMBER] Prmtop for protein + 2 identical ligands has wrong dihedral parameters for the second ligand. LEaP bug? Mariano Curti
- Re: [AMBER] antechamber problem with negatively charged nitrogen David A Case
- Re: [AMBER] Perturbing charges David A Case
- Re: [AMBER] antechamber problem with negatively charged nitrogen Giorgos Lambrinidis
- [AMBER] Problem in AMBER18 Installation Mariangela Dametto
- Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations Vaibhav Dixit
- Re: [AMBER] Problem in AMBER18 Installation David A Case
- Re: [AMBER] Perturbing charges Delwakkada Liyanage, Senal Dinuka
- [AMBER] Mimimization error Renato Araujo
- Re: [AMBER] constant pH MD in explicit solvent Cruzeiro,Vinicius Wilian D
- Re: [AMBER] constant pH error Cruzeiro,Vinicius Wilian D
- Re: [AMBER] Mimimization error David A Case
- [AMBER] Is RTX 3080 compatible with Amber18 ? Setyanto Md
- [AMBER] Tri-coordination environment in zinc SATYAJIT KHATUA
- Re: [AMBER] Tri-coordination environment in zinc Zoran
Saturday, 19 September 2020
- [AMBER] Formation of a cyclic peptide RIMJHIM MORAL
- Re: [AMBER] Formation of a cyclic peptide Bill Ross
- [AMBER] Stuck at the heating stage Jisha B
- Re: [AMBER] Stuck at the heating stage Bill Ross
- Re: [AMBER] Stuck at the heating stage Jisha B
- Re: [AMBER] Stuck at the heating stage Bill Ross
- Re: [AMBER] Formation of a cyclic peptide David A Case
- Re: [AMBER] Stuck at the heating stage David A Case
- Re: [AMBER] constant pH error Kolattukudy P. Santo
- [AMBER] constant pH MD in explicit solvent SATYAJIT KHATUA
- [AMBER] Tri-coordination environment in zinc SATYAJIT KHATUA
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Vaibhav Dixit
Sunday, 20 September 2020
- [AMBER] RMSF plot error Fatemeh Arabi
- Re: [AMBER] RMSF plot error David A Case
- Re: [AMBER] Perturbing charges David A Case
- Re: [AMBER] antechamber problem with negatively charged nitrogen David A Case
- Re: [AMBER] Perturbing charges Debarati DasGupta
- [AMBER] MMPBSA binding energy was positive for charged ligand Nada Afiva
Monday, 21 September 2020
- Re: [AMBER] antechamber problem with negatively charged nitrogen Giorgos Lambrinidis
- [AMBER] MMPBSA.py error Asmi Mahmood
- [AMBER] How to place oxygen molecules in tunnels of protein to calculate PMF Muhammad tariq
- Re: [AMBER] MMPBSA binding energy was positive for charged ligand David A Case
- Re: [AMBER] antechamber problem with negatively charged nitrogen David A Case
- Re: [AMBER] MMPBSA binding energy was positive for charged ligand Nada Afiva
- [AMBER] [CPHMD] invalid reference to variable in NAMELIST input, CPIN file cprivat.ub.edu
- Re: [AMBER] [CPHMD] invalid reference to variable in NAMELIST input, CPIN file Cruzeiro,Vinicius Wilian D
- Re: [AMBER] Perturbing charges Delwakkada Liyanage, Senal Dinuka
- Re: [AMBER] Perturbing charges Debarati DasGupta
- Re: [AMBER] Perturbing charges Delwakkada Liyanage, Senal Dinuka
- [AMBER] How to recopile with new version of CUDA Camila Clemente
- Re: [AMBER] How to recopile with new version of CUDA David Cerutti
- [AMBER] amber18 installation error Nisha Amarnath Jonniya
- Re: [AMBER] [CPHMD] invalid reference to variable in NAMELIST input, CPIN file cprivat.ub.edu
- Re: [AMBER] amber18 installation error Gustaf Olsson
- Re: [AMBER] amber18 installation error Nisha Amarnath Jonniya
Tuesday, 22 September 2020
- Re: [AMBER] amber18 installation error Gustaf Olsson
- Re: [AMBER] amber18 installation error Nisha Amarnath Jonniya
- Re: [AMBER] amber18 installation error Gustaf Olsson
- Re: [AMBER] Formation of a cyclic peptide Dr. Anselm Horn
- [AMBER] autoimage for grid analysis with cpptraj Gustaf Olsson
- Re: [AMBER] amber18 installation error David A Case
- Re: [AMBER] autoimage for grid analysis with cpptraj David A Case
- Re: [AMBER] amber18 installation error Elvis Martis
- Re: [AMBER] amber18 installation error Elvis Martis
- Re: [AMBER] amber18 installation error Nisha Amarnath Jonniya
- Re: [AMBER] autoimage for grid analysis with cpptraj Gustaf Olsson
- Re: [AMBER] MMPBSA binding energy was positive for charged ligand neildancer
- Re: [AMBER] autoimage for grid analysis with cpptraj Daniel Roe
- [AMBER] umbrella sampling protein Ramin Mehrani
- Re: [AMBER] umbrella sampling protein David A Case
- Re: [AMBER] umbrella sampling protein Feng Pan
- [AMBER] How does tleap detect improper torsions? Brian Radak
- Re: [AMBER] How does tleap detect improper torsions? David A Case
- [AMBER] how to keep Cl/Br/I ion in particular place Nisha Amarnath Jonniya
- [AMBER] tutorials restructured and ConstpH/redox tutorial pages not accessible Vaibhav Dixit
- Re: [AMBER] autoimage for grid analysis with cpptraj Gustaf Olsson
Wednesday, 23 September 2020
- [AMBER] french version aishen
- Re: [AMBER] autoimage for grid analysis with cpptraj Daniel Roe
- [AMBER] Coordinate resetting cannot be accomplished -reg R A Jeyaram 16PHD0482
- Re: [AMBER] Stuck at the heating stage Daniel Roe
- Re: [AMBER] Coordinate resetting cannot be accomplished -reg Daniel Roe
- Re: [AMBER] Regarding help in installation (LINUX ubuntu) Daniel Roe
- Re: [AMBER] Coordinate resetting cannot be accomplished -reg Bill Ross
- Re: [AMBER] tutorials restructured and ConstpH/redox tutorial pages not accessible Maria Nagan
- Re: [AMBER] tutorials restructured and ConstpH/redox tutorial pages not accessible Vaibhav Dixit
- Re: [AMBER] How does tleap detect improper torsions? Brian Radak
- Re: [AMBER] french version Dr. Anselm Horn
- Re: [AMBER] tutorials restructured and ConstpH/redox tutorial pages not accessible Daniel Roe
- Re: [AMBER] umbrella sampling protein Ramin Mehrani
- Re: [AMBER] How does tleap detect improper torsions? Matias Machado
- [AMBER] Heme parameters Siavoush Dastmalchi
- Re: [AMBER] tutorials restructured and ConstpH/redox tutorial pages not accessible Vaibhav Dixit
- [AMBER] Fwd: usage of nmr (between COMs) restraints with pmem.cuda Dmitry Karlov
- Re: [AMBER] adding lysyl-phosphatidylglycerol and cardiolipin Stephan Schott
- [AMBER] xleap aishen
- [AMBER] MMPBSA.py error for mismatch NATOMS Asmi Mahmood
Thursday, 24 September 2020
- Re: [AMBER] xleap Gustaf Olsson
- Re: [AMBER] xleap aishen
- Re: [AMBER] xleap aishen
- Re: [AMBER] xleap Gustaf Olsson
- [AMBER] water strip -reg R A Jeyaram 16PHD0482
- Re: [AMBER] adding lysyl-phosphatidylglycerol and cardiolipin Chetna Tyagi
- Re: [AMBER] water strip -reg Daniel Roe
- [AMBER] Line minimizer aborted Ramanathan Rajesh
- Re: [AMBER] Heme parameters David A Case
- Re: [AMBER] Heme parameters Siavoush Dastmalchi
- Re: [AMBER] How does tleap detect improper torsions? Brian Radak
- Re: [AMBER] How does tleap detect improper torsions? Bill Ross
- Re: [AMBER] How does tleap detect improper torsions? David A Case
- [AMBER] Two sets of restraints on minimization? Gustavo Seabra
- [AMBER] usage of nmr (between COMs) restraints with pmem.cuda Dmitry Karlov
- Re: [AMBER] Two sets of restraints on minimization? David A Case
- [AMBER] RESTARTED DUE TO LINMIN FAILURE Xinye Wang
- Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE Elvis Martis
- Re: [AMBER] How does tleap detect improper torsions? Matias Machado
- Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE Xinye Wang
- Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE Elvis Martis
- Re: [AMBER] How does tleap detect improper torsions? Bill Ross
Friday, 25 September 2020
- Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE David A Case
- Re: [AMBER] Two sets of restraints on minimization? Gustavo Seabra
- Re: [AMBER] umbrella sampling protein Feng Pan
- Re: [AMBER] finding number of atoms within a radius Daniel Roe
- [AMBER] Fwd: RESTARTED DUE TO LINMIN FAILURE Maschietto, Federica
- Re: [AMBER] Fwd: RESTARTED DUE TO LINMIN FAILURE Hector A. Baldoni
Saturday, 26 September 2020
- Re: [AMBER] Fwd: RESTARTED DUE TO LINMIN FAILURE David A Case
- Re: [AMBER] MMPBSA.py error for mismatch NATOMS Jason Swails
- [AMBER] Netcdf trajectory in pymol? Jenny 148
Sunday, 27 September 2020
- Re: [AMBER] Netcdf trajectory in pymol? Kenneth Huang
- [AMBER] A100 and RTX3090 Benchmarks Ross Walker
- Re: [AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane
Monday, 28 September 2020
- Re: [AMBER] Fw: covalent molecule and modified residue parameters David A Case
- Re: [AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane
- [AMBER] Make some of RNA bases as DNA in leap Athena N
- Re: [AMBER] Parametrization of GTP and terminal phosphate of DNA Jenny 148
- [AMBER] Polyproline abmd tutorial gives vlimit error SHAUNAK BADANI
- Re: [AMBER] Make some of RNA bases as DNA in leap David A Case
- Re: [AMBER] Make some of RNA bases as DNA in leap Athena N
Tuesday, 29 September 2020
- [AMBER] PMF calculation somdev pahari
Monday, 28 September 2020
- Re: [AMBER] PMF calculation Dickson, Callum
- Re: [AMBER] Make some of RNA bases as DNA in leap David A Case
- Re: [AMBER] Parametrization of GTP and terminal phosphate of DNA David A Case
- Re: [AMBER] xleap David A Case
Tuesday, 29 September 2020
- Re: [AMBER] PMF calculation somdev pahari
- [AMBER] MMPBSA.py.MPI installation problem in Amber20 Liao
- [AMBER] REMD Trajectory Processing Aravind R
- Re: [AMBER] MMPBSA.py.MPI installation problem in Amber20 Elvis Martis
- Re: [AMBER] xleap Gustaf Olsson
- Re: [AMBER] xleap Bill Ross
- [AMBER] Query regarding Dialanine peptide 2d ABMD tutorial in the NFE category SHAUNAK BADANI
- Re: [AMBER] A100 and RTX3090 Benchmarks xmgign.126.com
- Re: [AMBER] xleap Gustaf Olsson
- Re: [AMBER] xleap Bill Ross
- Re: [AMBER] xleap aishen
- Re: [AMBER] REMD Trajectory Processing Daniel Roe
- Re: [AMBER] xleap David A Case
- Re: [AMBER] xleap Gustaf Olsson
- Re: [AMBER] xleap aishen
- Re: [AMBER] xleap aishen
- Re: [AMBER] xleap Gustaf Olsson
- Re: [AMBER] REMD Trajectory Processing Carlos Simmerling
- Re: [AMBER] xleap aishen
Wednesday, 30 September 2020
- [AMBER] Problem with metalpdb2mol2.py script Siavoush Dastmalchi
- [AMBER] Query regarding Dialanine peptide 2d ABMD tutorial in the NFE category Madhur Aggarwal
Tuesday, 29 September 2020
- [AMBER] AmberMdPrep github cpptraj not sourced Vaibhav Dixit
Wednesday, 30 September 2020
- [AMBER] Modification of dihedral torsion potential h_sahakyan.mb.sci.am
- [AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am
- Re: [AMBER] AmberMdPrep github cpptraj not sourced Vaibhav Dixit
- Re: [AMBER] AmberMdPrep github cpptraj not sourced Daniel Roe
- Re: [AMBER] AmberMdPrep github cpptraj not sourced Vaibhav Dixit
- Re: [AMBER] A100 and RTX3090 Benchmarks Hashemi, Mohtadin
- Re: [AMBER] AmberMdPrep github cpptraj not sourced Vaibhav Dixit
- [AMBER] Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT Nick Palmer
- [AMBER] Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT Nick Palmer
- Re: [AMBER] controversy in PBSA and GBSA results Ray Luo
- Re: [AMBER] controversy in PBSA and GBSA results Ray Luo

Last message date: Wed Sep 30 2020 - 22:30:02 PDT
Archived on: Fri Apr 19 2024 - 05:55:46 PDT

Amber Archive Sep 2020 by date