Amber Archive Jul 2015: by date

Tuesday, 30 June 2015
- Re: [AMBER] Output format in sander Brent Krueger
Wednesday, 1 July 2015
- [AMBER] Why the entropy contribution from quasi-harmonic and normal mode methods are so different? wliu
- Re: [AMBER] Rms fitting to a reference structure with a differnt number atoms to top file George Green
- Re: [AMBER] Why the entropy contribution from quasi-harmonic and normal mode methods are so different? Hannes Loeffler
- Re: [AMBER] Output format in sander Jason Swails
- Re: [AMBER] Output format in sander David A Case
- Re: [AMBER] Compile Failure David A Case
- [AMBER] Lipid diffusion in cpptraj Life Sciences Inc
- Re: [AMBER] Output format in sander Jason Swails
- Re: [AMBER] Output format in sander Jason Swails
- [AMBER] leap changes residue order Ignacio Faustino
- Re: [AMBER] leap changes residue order Hannes Loeffler
- Re: [AMBER] leap changes residue order Jason Swails
- Re: [AMBER] Compile Failure Jim Wu
- [AMBER] water networks and bridge option of the hbond command in cpptraj Vlad Cojocaru
- [AMBER] QM/MM Equilibration Troubles Brittany Boykin
- Re: [AMBER] QM/MM Equilibration Troubles Brian Radak
- [AMBER] anisotropic vs. semi-isotropic membrane simulations Naomi Rose Latorraca
- Re: [AMBER] anisotropic vs. semi-isotropic membrane simulations Ross Walker
- Re: [AMBER] Why the entropy contribution from quasi-harmonic and normal mode methods are so different? wliu
Thursday, 2 July 2015
- [AMBER] Ambertools15 installation without Amber ANWESHA SARKAR
- Re: [AMBER] Ambertools15 installation without Amber Gerald Monard
- Re: [AMBER] Ambertools15 installation without Amber ANWESHA SARKAR
- Re: [AMBER] Ambertools15 installation without Amber Gerald Monard
- Re: [AMBER] Ambertools15 installation without Amber ANWESHA SARKAR
- Re: [AMBER] Ambertools15 installation without Amber Gerald Monard
- [AMBER] kclust help Harmeet Kaur
- Re: [AMBER] anisotropic vs. semi-isotropic membrane simulations Jason Swails
- Re: [AMBER] folding RNA using SGLD Asmita Gupta
- Re: [AMBER] Compile Failure David A Case
- Re: [AMBER] anisotropic vs. semi-isotropic membrane simulations David A Case
- [AMBER] another leap inconsistency Hannes Loeffler
- [AMBER] Chlorophyll A .mol2 file Ofir Tal
- Re: [AMBER] another leap inconsistency Jason Swails
- Re: [AMBER] Lipid diffusion in cpptraj Daniel Roe
- Re: [AMBER] Cpptraj failure Daniel Roe
- Re: [AMBER] water networks and bridge option of the hbond command in cpptraj Daniel Roe
- Re: [AMBER] leap changes residue order Ignacio Faustino
- Re: [AMBER] kclust help Daniel Roe
- Re: [AMBER] Output format in sander John Dood
- [AMBER] Cpptraj able to identify coordinates written by VMD? Karl Debiec
- Re: [AMBER] Cpptraj able to identify coordinates written by VMD? Brian Radak
- Re: [AMBER] Cpptraj able to identify coordinates written by VMD? Thomas Cheatham
- [AMBER] Regarding melt curve MOHD HOMAIDUR RAHMAN
- Re: [AMBER] Regarding melt curve nhai.wn
Friday, 3 July 2015
- [AMBER] help in make .prepin file Robin Jain
- [AMBER] How to set interatomic distance restraint? Michael Shokhen
- Re: [AMBER] help in make .prepin file David A Case
- Re: [AMBER] How to set interatomic distance restraint? David A Case
- [AMBER] Question about AMBER energy decomposition Lee-Ping Wang
- Re: [AMBER] another leap inconsistency hannes.loeffler.stfc.ac.uk
- Re: [AMBER] Question about AMBER energy decomposition Jason Swails
- [AMBER] extract coordinates of a specific atom Morteza Chehel Amirani
- Re: [AMBER] extract coordinates of a specific atom Nhai
Saturday, 4 July 2015
- Re: [AMBER] Question about AMBER energy decomposition Lee-Ping Wang
- [AMBER] charmmlipid2amber.py Ramin Ekhteiari
- Re: [AMBER] Question about AMBER energy decomposition Jason Swails
Sunday, 5 July 2015
- Re: [AMBER] How to set interatomic distance restraint? Michael Shokhen
- Re: [AMBER] How to set interatomic distance restraint? David A Case
Monday, 6 July 2015
- [AMBER] NOESY volumes restraints Eugene Sviridov
- [AMBER] assigning atom type and charge Sanjib Paul
- Re: [AMBER] assigning atom type and charge Jason Swails
- [AMBER] PME large NFFT John Dood
- Re: [AMBER] NOESY volumes restraints David A Case
- Re: [AMBER] PME large NFFT Jason Swails
- Re: [AMBER] How to set interatomic distance restraint? Michael Shokhen
- Re: [AMBER] How to set interatomic distance restraint? Jason Swails
- [AMBER] amber topology file for cytochrome c covalently bond to Heme Shoresh Shafei
- [AMBER] Reference energies for Explicit solvent CpHMD Arjun Sharma
- Re: [AMBER] Reference energies for Explicit solvent CpHMD Jason Swails
Tuesday, 7 July 2015
- [AMBER] cpptraj: bounds command -> grid Thomas Fox
- [AMBER] cpptraj: rmsd problem Thomas Fox
- Re: [AMBER] cpptraj: bounds command -> grid Daniel Roe
- Re: [AMBER] cpptraj: rmsd problem Daniel Roe
- [AMBER] Lipid linked to a peptide Arnoult, Eric [JRDUS]
- Re: [AMBER] Lipid linked to a peptide David A Case
- Re: [AMBER] amber topology file for cytochrome c covalently bond to Heme David A Case
- [AMBER] About python usage in AmberTools Juan Eiros Zamora
- Re: [AMBER] About python usage in AmberTools Hai Nguyen
- Re: [AMBER] About python usage in AmberTools Jason Swails
- Re: [AMBER] About python usage in AmberTools Eiros Zamora, Juan
- Re: [AMBER] About python usage in AmberTools Jason Swails
- Re: [AMBER] About python usage in AmberTools Hai Nguyen
- [AMBER] NumPy Import Error for MCPB.py on Amber15 Eleftherios A P Lambros
- Re: [AMBER] NumPy Import Error for MCPB.py on Amber15 Takeshi Baba
- Re: [AMBER] NumPy Import Error for MCPB.py on Amber15 Hai Nguyen
- [AMBER] issue using CUDA+MPI+OpenMP Éric Germaneau
Wednesday, 8 July 2015
- Re: [AMBER] issue using CUDA+MPI+OpenMP Gerald Monard
- [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. giulia palermo
- [AMBER] help in amber Robin Jain
- Re: [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. Jason Swails
- Re: [AMBER] help in amber Jason Swails
- Re: [AMBER] About python usage in AmberTools Juan Eiros Zamora
- Re: [AMBER] About python usage in AmberTools Jason Swails
- Re: [AMBER] About python usage in AmberTools Juan Eiros Zamora
- Re: [AMBER] About python usage in AmberTools Jason Swails
- Re: [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. giulia palermo
- Re: [AMBER] About python usage in AmberTools Juan Eiros Zamora
- Re: [AMBER] About python usage in AmberTools Hai Nguyen
- Re: [AMBER] About python usage in AmberTools Hai Nguyen
- Re: [AMBER] About python usage in AmberTools Jason Swails
- Re: [AMBER] Lipid diffusion in cpptraj Life Sciences Inc
- Re: [AMBER] issue using CUDA+MPI+OpenMP Éric Germaneau
- Re: [AMBER] issue using CUDA+MPI+OpenMP David A Case
- Re: [AMBER] issue using CUDA+MPI+OpenMP Éric Germaneau
Thursday, 9 July 2015
- [AMBER] problem in amber Robin Jain
- Re: [AMBER] How to set interatomic distance restraint? Michael Shokhen
- [AMBER] Unexpected prochirality change from si to re during MD simulation Michael Shokhen
- Re: [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. FyD
- Re: [AMBER] assigning atom type and charge FyD
- [AMBER] Namdenergy problems with non-standard amino acids Clavel
- Re: [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. Brent Krueger
- [AMBER] Problem in loading the pdb file Harshala Haldankar
- Re: [AMBER] issue using CUDA+MPI+OpenMP Ross Walker
- Re: [AMBER] problem in amber Jason Swails
- Re: [AMBER] Namdenergy problems with non-standard amino acids Jason Swails
- Re: [AMBER] Problem in loading the pdb file Jason Swails
- Re: [AMBER] issue using CUDA+MPI+OpenMP Brent Krueger
- Re: [AMBER] issue using CUDA+MPI+OpenMP Jason Swails
- [AMBER] parameters dATP Francesca Cardamone
- [AMBER] articles published for ff14SB and GBneck2 Carlos Simmerling
- Re: [AMBER] issue using CUDA+MPI+OpenMP Scott Le Grand
- Re: [AMBER] Lipid diffusion in cpptraj Daniel Roe
- Re: [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. giulia palermo
- Re: [AMBER] Explicit Solvent Constant pH MD Rahul Ramesh
- Re: [AMBER] Explicit Solvent Constant pH MD Jason Swails
- Re: [AMBER] Explicit Solvent Constant pH MD Alan
- Re: [AMBER] AMBER Digest, Vol 1274, Issue 1 Eleftherios A P Lambros
- Re: [AMBER] AMBER Digest, Vol 1274, Issue 1 Eleftherios A P Lambros
- Re: [AMBER] AMBER Digest, Vol 1274, Issue 1 Hai Nguyen
- [AMBER] Magnesium in MMGBSA Ahmed Ayoub
- [AMBER] ESURF term in MMGBSA Ahmed Ayoub
- Re: [AMBER] Problem in loading the pdb file Harshala Haldankar
Friday, 10 July 2015
- [AMBER] Order of the atom in prep ourput of antechamber Nicholus Bhattacharjee
- [AMBER] problems on amoeba force filed implemented in amber fjliu
- Re: [AMBER] Order of the atom in prep ourput of antechamber Hannes Loeffler
- [AMBER] Changing NMR restraint weights Oliver Grant
- Re: [AMBER] Order of the atom in prep ourput of antechamber Thomas Fox
- [AMBER] question about advanced tutorial 3 Mohsen Zakeri
- Re: [AMBER] question about advanced tutorial 3 Juan Eiros Zamora
- [AMBER] FEW tutorial Mohsen Zakeri
- Re: [AMBER] NOESY volumes restraints Eugene Sviridov
- Re: [AMBER] Problem in loading the pdb file Jason Swails
- Re: [AMBER] FEW tutorial Hannes Loeffler
- Re: [AMBER] problems on amoeba force filed implemented in amber Jason Swails
- Re: [AMBER] Magnesium in MMGBSA Jason Swails
- Re: [AMBER] ESURF term in MMGBSA Jason Swails
- Re: [AMBER] articles published for ff14SB and GBneck2 Vlad Cojocaru
- [AMBER] molecules split apart during MD Lara rajam
- Re: [AMBER] molecules split apart during MD Jason Swails
- [AMBER] molecules split apart during MD Kenneth Huang
- [AMBER] atom mapping Gard Nelson
- [AMBER] compare two trajectories Xing
- Re: [AMBER] compare two trajectories Hai Nguyen
- [AMBER] FATAL: Atom () does not have a type???? Evans, Shalton
- [AMBER] About charge derivation for enantiomers Tommaso Casalini
- Re: [AMBER] FATAL: Atom () does not have a type???? Kenneth Huang
- Re: [AMBER] FATAL: Atom () does not have a type???? Evans, Shalton
- [AMBER] pmemd.cuda.MPI error - integer divide by zero Bill Miller III
- Re: [AMBER] Explicit Solvent Constant pH MD Rahul Ramesh
- [AMBER] FATAL: Atom () does not have a type???? Kenneth Huang
- Re: [AMBER] pmemd.cuda.MPI error - integer divide by zero David A Case
Saturday, 11 July 2015
- [AMBER] pmemd.cuda implementation of sgld Asmita Gupta
- [AMBER] About charge derivation for enantiomeric molecules Tommaso Casalini
- Re: [AMBER] Order of the atom in prep ourput of antechamber David A Case
- Re: [AMBER] pmemd.cuda.MPI error - integer divide by zero Jason Swails
- Re: [AMBER] About charge derivation for enantiomeric molecules case
- Re: [AMBER] About charge derivation for enantiomeric molecules Casalini Tommaso
- Re: [AMBER] Explicit Solvent Constant pH MD Jason Swails
- Re: [AMBER] pmemd.cuda implementation of sgld Daniel Roe
- [AMBER] Query about adding hydrogens anu chandra
- Re: [AMBER] Query about adding hydrogens Bill Ross
Sunday, 12 July 2015
- Re: [AMBER] atom mapping Daniel Roe
- [AMBER] Producing Decoys with AmberTools Mohsen Zakeri
Monday, 13 July 2015
- Re: [AMBER] NOESY volumes restraints David A Case
- Re: [AMBER] Unexpected prochirality change from si to re during MD simulation David A Case
- Re: [AMBER] Changing NMR restraint weights David A Case
- [AMBER] Problem in Using the Average Command in Cpptraj Robert Molt
- Re: [AMBER] Problem in Using the Average Command in Cpptraj Jason Swails
- Re: [AMBER] Problem in Using the Average Command in Cpptraj Daniel Roe
- Re: [AMBER] Problem in Using the Average Command in Cpptraj Robert Molt
- Re: [AMBER] Cpptraj failure Lin Song
- [AMBER] Relaxing a heme molecule Amber Maharaj
- Re: [AMBER] Lipid diffusion in cpptraj Life Sciences Inc
- Re: [AMBER] Relaxing a heme molecule case
- Re: [AMBER] Lipid diffusion in cpptraj hannes.loeffler.stfc.ac.uk
Tuesday, 14 July 2015
- [AMBER] help in making xyz file Robin Jain
- Re: [AMBER] problems on amoeba force filed implemented in amber fjliu
- Re: [AMBER] problems on amoeba force filed implemented in amber Jason Swails
- Re: [AMBER] help in making xyz file Jason Swails
- Re: [AMBER] help in making xyz file David A Case
- Re: [AMBER] Changing NMR restraint weights Oliver Grant
- Re: [AMBER] Lipid diffusion in cpptraj Daniel Roe
- Re: [AMBER] Changing NMR restraint weights David A Case
- [AMBER] Accelerated md for protein dna complex with modified residue Muthukumaran R
- [AMBER] ETOT drift and nscm in NVE for calculation of diffusion CHAMI F.
- Re: [AMBER] pmemd.cuda.MPI error - integer divide by zero Bill Miller III
- Re: [AMBER] problems on amoeba force filed implemented in amber fjliu
Wednesday, 15 July 2015
- [AMBER] strange output from vacuum minimization Albert
- [AMBER] MMPBSA.py API quasi-harmonic error D.J. Pattinson
- [AMBER] MPI compiling failed Albert
- Re: [AMBER] strange output from vacuum minimization David A Case
- Re: [AMBER] MPI compiling failed David A Case
- Re: [AMBER] MPI compiling failed Albert
- [AMBER] test failed but still work Albert
- [AMBER] setting up a MD simulation using AMBER Amber mail
- Re: [AMBER] Accelerated md for protein dna complex with modified residue Vlad Cojocaru
- [AMBER] NetCDF file Marta Wisniewska
- Re: [AMBER] NetCDF file Hannes Loeffler
- Re: [AMBER] NetCDF file Hai Nguyen
- Re: [AMBER] NetCDF file Marcus Arieno
- Re: [AMBER] NetCDF file Hannes Loeffler
- Re: [AMBER] test failed but still work David A Case
- Re: [AMBER] setting up a MD simulation using AMBER David A Case
- Re: [AMBER] problems on amoeba force filed implemented in amber Brian Radak
- Re: [AMBER] MPI compiling failed Jason Swails
- Re: [AMBER] test failed but still work Jason Swails
- Re: [AMBER] test failed but still work Albert
- Re: [AMBER] test failed but still work Albert
- Re: [AMBER] Relaxing a heme molecule Amber Maharaj
- Re: [AMBER] test failed but still work case
- [AMBER] Error in writing .lib file Elvis Martis
- [AMBER] Coordinate resetting (SHAKE) cannot be accomplished Vahid Kshani
- Re: [AMBER] test failed but still work Albert
Thursday, 16 July 2015
- [AMBER] AMBER error : Coordinate resetting (SHAKE) cannot be accomplish ed MASAOKI FUJII
- [AMBER] running sgld in explicit solvent Asmita Gupta
- Re: [AMBER] Error in writing .lib file David A Case
- Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished David A Case
- Re: [AMBER] test failed but still work David A Case
- Re: [AMBER] AMBER error : Coordinate resetting (SHAKE) cannot be accomplish ed David A Case
- Re: [AMBER] running sgld in explicit solvent David A Case
- Re: [AMBER] test failed but still work Albert
- Re: [AMBER] running sgld in explicit solvent Asmita Gupta
- [AMBER] RESP Fit to Atomic Multipoles Yip Yew Mun
- Re: [AMBER] RESP Fit to Atomic Multipoles ymei
- Re: [AMBER] RESP Fit to Atomic Multipoles Yip Yew Mun
- Re: [AMBER] svdcmp in sander/ncsu-rmsd.F90 (AmberTools15) is sensitive to higher optimizations, suggest using lapack routine instead David A Case
- Re: [AMBER] svdcmp in sander/ncsu-rmsd.F90 (AmberTools15) is sensitive to higher optimizations, suggest using lapack routine instead Åke Sandgren
- Re: [AMBER] NMR restraints with pmemd.cuda problem Needham, Perri
- [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI M Olivia Kim
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI Daniel Mermelstein
- [AMBER] MCPB.py ValueError Eleftherios A P Lambros
- Re: [AMBER] MCPB.py ValueError Takeshi Baba
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI hannes.loeffler.stfc.ac.uk
Friday, 17 July 2015
- Re: [AMBER] Error in writing .lib file Elvis Martis
- [AMBER] frames in mmpbsa.py Albert
- [AMBER] Deleting multiple atoms in xleap jacob wick
- [AMBER] no FINAL_RESULTS_MMPBSA.dat generated Albert
- Re: [AMBER] Deleting multiple atoms in xleap jacob wick
- [AMBER] countless warnning Albert
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI Olivia Pierce
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI hannes.loeffler.stfc.ac.uk
- Re: [AMBER] countless warnning Ray Luo, Ph.D.
- Re: [AMBER] frames in mmpbsa.py Jason Swails
- Re: [AMBER] no FINAL_RESULTS_MMPBSA.dat generated Jason Swails
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI Olivia Pierce
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI hannes.loeffler.stfc.ac.uk
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI Olivia Pierce
- [AMBER] illegal memory access in amber GPU simulations Latorraca, Naomi Rose
- Re: [AMBER] illegal memory access in amber GPU simulations Ross Walker
- [AMBER] Problem in saving parameter/topology and coordinate file. Harshala Haldankar
Saturday, 18 July 2015
- Re: [AMBER] Problem in saving parameter/topology and coordinate file. Bill Ross
- [AMBER] help in resp charge Robin Jain
- Re: [AMBER] help in resp charge hannes.loeffler.stfc.ac.uk
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI hannes.loeffler.stfc.ac.uk
- Re: [AMBER] Deleting multiple atoms in xleap Jason Swails
Sunday, 19 July 2015
- [AMBER] help in box size detremination Robin Jain
- [AMBER] help in box size determination Robin Jain
- Re: [AMBER] frames in mmpbsa.py Albert
Monday, 20 July 2015
- [AMBER] installation without ambertools Asmita Gupta
- [AMBER] Distance restraint in AMBER 14 and GPU Lionel Sacconnay
- Re: [AMBER] Problem in saving parameter/topology and coordinate file. Harshala Haldankar
- [AMBER] incorrect determination of atomic number for atom Cl in tleap Ye Renlo
- [AMBER] Problem cpptraj Bridging H-Bond analysis Beuerle, Matthias
- Re: [AMBER] help in box size determination David A Case
- Re: [AMBER] frames in mmpbsa.py Jason Swails
- Re: [AMBER] Distance restraint in AMBER 14 and GPU David A Case
- Re: [AMBER] installation without ambertools Jason Swails
- Re: [AMBER] incorrect determination of atomic number for atom Cl in tleap David A Case
- Re: [AMBER] Problem cpptraj Bridging H-Bond analysis Daniel Roe
- Re: [AMBER] Problem in saving parameter/topology and coordinate file. Bill Ross
- [AMBER] CPPTRAJ - Filtering frames based on lowest of the two RMSD values Stevens, David
- Re: [AMBER] CPPTRAJ - Filtering frames based on lowest of the two RMSD values Hai Nguyen
- [AMBER] Gaff Parameters Si Sharapa
- Re: [AMBER] CPPTRAJ - Filtering frames based on lowest of the two RMSD values Daniel Roe
- [AMBER] GTX980Ti's now supported for AMBER and Exxact GTX780Tis available at discounted prices Ross Walker
- [AMBER] MCPB.py Value / Syntax error Eleftherios A P Lambros
- [AMBER] qm-mmgbsa error Ayesha Fatima
Tuesday, 21 July 2015
- Re: [AMBER] Immediate Postdoctoral Position Opening In Dr. Khaled Barakat’s Lab, Faculty Of Pharmacy, University Of Alberta Ayesha Fatima
- Re: [AMBER] GTX980Ti's now supported for AMBER and Exxact GTX780Tis available at discounted prices Albert
- [AMBER] Unchanged coordinates in leap mish
- Re: [AMBER] GTX980Ti's now supported for AMBER and Exxact GTX780Tis available at discounted prices David Abia
- [AMBER] PCA and motions visualization antonio.coluccia.uniroma1.it
- [AMBER] "nstlim" is not reflected correctly in REMD with pmemd.MPI kurisaki
- Re: [AMBER] "nstlim" is not reflected correctly in REMD with pmemd.MPI kurisaki
- Re: [AMBER] Problem in saving parameter/topology and coordinate file. David A Case
- Re: [AMBER] Gaff Parameters Si David A Case
- Re: [AMBER] Unchanged coordinates in leap David A Case
- [AMBER] MCPB.py N terminal error Jon Uranga
- Re: [AMBER] "nstlim" is not reflected correctly in REMD with pmemd.MPI Gerald Monard
- Re: [AMBER] MCPB.py N terminal error Takeshi Baba
- [AMBER] Testing the titratable group definition CpHMD Arjun Sharma
- [AMBER] hbond cpptraj Lara rajam
- Re: [AMBER] Testing the titratable group definition CpHMD Jason Swails
- Re: [AMBER] PCA and motions visualization Jason Swails
- Re: [AMBER] qm-mmgbsa error Jason Swails
- Re: [AMBER] hbond cpptraj Daniel Roe
- [AMBER] Error in loading inpcrd file in sander Mohsen Zakeri
- Re: [AMBER] Error in loading inpcrd file in sander Hai Nguyen
- Re: [AMBER] Error in loading inpcrd file in sander Daniel Roe
- Re: [AMBER] Error in loading inpcrd file in sander Mohsen Zakeri
- Re: [AMBER] Error in loading inpcrd file in sander Mohsen Zakeri
- Re: [AMBER] Error in loading inpcrd file in sander Daniel Roe
- Re: [AMBER] Error in loading inpcrd file in sander Mohsen Zakeri
- Re: [AMBER] ETOT drift and nscm in NVE for calculation of diffusion Jason Swails
- Re: [AMBER] PCA and motions visualization Daniel Roe
- Re: [AMBER] qm-mmgbsa error Ayesha Fatima
- Re: [AMBER] qm-mmgbsa error Jason Swails
- Re: [AMBER] CpptrajPairDist bharat lakhani
- Re: [AMBER] qm-mmgbsa error Ayesha Fatima
Wednesday, 22 July 2015
- [AMBER] QM/GBSA calculation failed Albert
- [AMBER] Periodic Box Size and Charge Determination Aronica, Pietro
- Re: [AMBER] QM/GBSA calculation failed Jason Swails
- Re: [AMBER] Periodic Box Size and Charge Determination Jason Swails
- Re: [AMBER] Periodic Box Size and Charge Determination Aronica, Pietro
- Re: [AMBER] Periodic Box Size and Charge Determination Jason Swails
- Re: [AMBER] QM/GBSA calculation failed Albert
- Re: [AMBER] QM/GBSA calculation failed Jason Swails
- [AMBER] Explicit solvent pH-REMD whb
- Re: [AMBER] Unchanged coordinates in leap mish
- Re: [AMBER] Periodic Box Size and Charge Determination Aronica, Pietro
- Re: [AMBER] Explicit solvent pH-REMD Jason Swails
- Re: [AMBER] Periodic Box Size and Charge Determination David A Case
- [AMBER] [cpptraj] Nativecontacts failing with long trajectory Juan Eiros Zamora
- Re: [AMBER] Monitoring GPU voltage Tru Huynh
- Re: [AMBER] Monitoring GPU voltage Tru Huynh
- Re: [AMBER] [cpptraj] Nativecontacts failing with long trajectory Daniel Roe
- Re: [AMBER] MCPB.py Value / Syntax error Pengfei Li
- Re: [AMBER] Monitoring GPU voltage Ross Walker
Thursday, 23 July 2015
- Re: [AMBER] [cpptraj] Nativecontacts failing with long trajectory Juan Eiros Zamora
- [AMBER] Amber for phophorylated residue Ziba Bahadori
- [AMBER] GTX Titan Xs slowing down after 200ns Mohamed Faizan Momin
- Re: [AMBER] GTX Titan Xs slowing down after 200ns Ross Walker
- Re: [AMBER] Amber for phophorylated residue David A Case
- Re: [AMBER] GTX Titan Xs slowing down after 200ns Mohamed Faizan Momin
- Re: [AMBER] GTX Titan Xs slowing down after 200ns Ross Walker
- Re: [AMBER] GTX Titan Xs slowing down after 200ns Scott Le Grand
- Re: [AMBER] GTX Titan Xs slowing down after 200ns Mohamed Faizan Momin
- Re: [AMBER] Amber for phophorylated residue Ziba Bahadori
- Re: [AMBER] GTX Titan Xs slowing down after 200ns Scott Le Grand
- Re: [AMBER] GTX Titan Xs slowing down after 200ns Mohamed Faizan Momin
- Re: [AMBER] [cpptraj] Nativecontacts failing with long trajectory Daniel Roe
- Re: [AMBER] CpptrajPairDist Daniel Roe
- Re: [AMBER] GTX Titan Xs slowing down after 200ns Ross Walker
- Re: [AMBER] GTX Titan Xs slowing down after 200ns David A Case
Friday, 24 July 2015
- [AMBER] Using TIP4PEW amber FF in NAMD peter.schmidtke.discngine.servier.com
- Re: [AMBER] [cpptraj] Nativecontacts failing with long trajectory Juan Eiros Zamora
- Re: [AMBER] Using TIP4PEW amber FF in NAMD peter.schmidtke.discngine.servier.com
- [AMBER] MPI_ABORT error Amber mail
- Re: [AMBER] MPI_ABORT error Amber mail
- Re: [AMBER] MPI_ABORT error Jason Swails
- Re: [AMBER] MPI_ABORT error Amber mail
- [AMBER] impose restraint mask for specific residues Latorraca, Naomi Rose
- Re: [AMBER] MPI_ABORT error Jason Swails
- Re: [AMBER] impose restraint mask for specific residues Jason Swails
- Re: [AMBER] MPI_ABORT error Amber mail
- Re: [AMBER] MPI_ABORT error Jason Swails
Saturday, 25 July 2015
- [AMBER] Speed of heating MD Amber mail
- [AMBER] GPU EVGA GTX 980 SC ACX M. Reza Ganjalikhany
- Re: [AMBER] GPU EVGA GTX 980 SC ACX Ross Walker
- Re: [AMBER] GPU EVGA GTX 980 SC ACX M. Reza Ganjalikhany
- Re: [AMBER] GPU EVGA GTX 980 SC ACX Ross Walker
- Re: [AMBER] Speed of heating MD Jason Swails
Sunday, 26 July 2015
- Re: [AMBER] Speed of heating MD Amber mail
- [AMBER] MD simulation: cis isomer of peptide bond Michael Shokhen
- Re: [AMBER] MD simulation: cis isomer of peptide bond Carlos Simmerling
- Re: [AMBER] MD simulation: cis isomer of peptide bond Michael Shokhen
- Re: [AMBER] MD simulation: cis isomer of peptide bond Carlos Simmerling
- Re: [AMBER] MD simulation: cis isomer of peptide bond Michael Shokhen
- Re: [AMBER] MD simulation: cis isomer of peptide bond Carlos Simmerling
- Re: [AMBER] MD simulation: cis isomer of peptide bond Michael Shokhen
Monday, 27 July 2015
- [AMBER] strange pbsa results Albert
- [AMBER] Targeted Molecular dynamics in Amber ROOPALI VERMA
- [AMBER] detecting and removing corrupted frames Thomas Evangelidis
- [AMBER] which solvent model to use with solvateCap peter.schmidtke.discngine.servier.com
- [AMBER] How to combine distance and torsion restraint? Michael Shokhen
- Re: [AMBER] detecting and removing corrupted frames Daniel Roe
- Re: [AMBER] strange pbsa results Jason Swails
- Re: [AMBER] How to combine distance and torsion restraint? Jason Swails
- Re: [AMBER] which solvent model to use with solvateCap Jason Swails
- Re: [AMBER] which solvent model to use with solvateCap peter.schmidtke.discngine.servier.com
- Re: [AMBER] which solvent model to use with solvateCap Jason Swails
- [AMBER] Prep file for chiral position Nicholus Bhattacharjee
- Re: [AMBER] Prep file for chiral position Carlos Simmerling
- Re: [AMBER] Prep file for chiral position Nicholus Bhattacharjee
- Re: [AMBER] Prep file for chiral position Carlos Simmerling
- [AMBER] MCPB.py mismatch error Eleftherios A P Lambros
Tuesday, 28 July 2015
- [AMBER] Cluster restraints Damiano Spadoni
- [AMBER] Restart of MMPBSA Osman, Roman
- Re: [AMBER] Restart of MMPBSA Jason Swails
- [AMBER] Issues with running simulation after ParmEd conversion Rohith Mohan
- Re: [AMBER] Cluster restraints David A Case
- Re: [AMBER] MCPB.py mismatch error Pengfei Li
- [AMBER] MM-GBSA at different temperature Shruti Koulgi
- [AMBER] Utilization of 3 GPUs suddenly drop to 0% and won't work any more 浅井賢
Wednesday, 29 July 2015
- Re: [AMBER] Issues with running simulation after ParmEd conversion Jason Swails
- Re: [AMBER] MM-GBSA at different temperature Jason Swails
- Re: [AMBER] Targeted Molecular dynamics in Amber Carlos Simmerling
- [AMBER] how to center on ligand? Albert
- Re: [AMBER] how to center on ligand? Jason Swails
- Re: [AMBER] Utilization of 3 GPUs suddenly drop to 0% and won't work any more Ross Walker
- Re: [AMBER] how to center on ligand? Daniel Roe
- Re: [AMBER] how to center on ligand? Albert
- Re: [AMBER] how to center on ligand? Jason Swails
- Re: [AMBER] Issues with running simulation after ParmEd conversion Rohith Mohan
- Re: [AMBER] Issues with running simulation after ParmEd conversion Jason Swails
- Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory bharat lakhani
- Re: [AMBER] how to center on ligand? Albert
Thursday, 30 July 2015
- [AMBER] Antechamber for boronic acid derivatives? Michael Shokhen
- Re: [AMBER] Fwd: NMR restraints with pmemd.cuda problem Miroslav Krepl
- Re: [AMBER] how to center on ligand? Daniel Roe
- [AMBER] Solvents that are not in a list. Sharapa
- Re: [AMBER] Gaff Parameters Si Sharapa
- Re: [AMBER] NMR restraints with pmemd.cuda problem Ross Walker
- [AMBER] multiple cpus per single gpu job Meij, Henk
- Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory Daniel Roe
- Re: [AMBER] multiple cpus per single gpu job Ross Walker
- Re: [AMBER] multiple cpus per single gpu job Meij, Henk
- Re: [AMBER] Issues with running simulation after ParmEd conversion Rohith Mohan
- Re: [AMBER] Issues with running simulation after ParmEd conversion Jason Swails
- Re: [AMBER] Lipid diffusion in cpptraj Life Sciences Inc
- Re: [AMBER] Utilization of 3 GPUs suddenly drop to 0% and won't work any more 浅井賢
- Re: [AMBER] Lipid diffusion in cpptraj hannes.loeffler.stfc.ac.uk
Friday, 31 July 2015
- [AMBER] Explicit-solvent-pH-REMD whb
- [AMBER] Regarding ADP molecule force fields Yogeeshwar Ajjugal
- Re: [AMBER] Explicit-solvent-pH-REMD Jason Swails
- Re: [AMBER] Regarding ADP molecule force fields Jason Swails
- [AMBER] mdfrc units Georgios Gerogiokas
- Re: [AMBER] mdfrc units Jason Swails
- Re: [AMBER] Utilization of 3 GPUs suddenly drop to 0% and won't work any more Ross Walker
- Re: [AMBER] Issues with running simulation after ParmEd conversion Rohith Mohan
- Re: [AMBER] MCPB.py mismatch error Pengfei Li

Last message date: Fri Jul 31 2015 - 14:00:05 PDT
Archived on: Fri Nov 15 2024 - 05:55:16 PST

Amber Archive Jul 2015 by date