Amber Archive Jun 2013 by thread
- Re: [AMBER] by pmemd.cuda runs Cenk \(Jenk\) Andac (Sat Jun 01 2013 - 03:05:31 PDT)
- [AMBER] Unfolding a protein using Accelerated Molecular Dynamics sunita gupta (Sat Jun 01 2013 - 04:11:51 PDT)
- [AMBER] search for a method name: 'targeted molecular dynamics'? Jan-Philip Gehrcke (Sat Jun 01 2013 - 07:08:36 PDT)
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Sat Jun 01 2013 - 11:26:16 PDT)
- [AMBER] Amber 12 bugfix 18 ? Marek Maly (Sat Jun 01 2013 - 11:22:53 PDT)
- [AMBER] To all K20 - K20x "positive" Amber users Marek Maly (Sat Jun 01 2013 - 13:22:21 PDT)
- [AMBER] Which is the best compiler to use with AMBER 12 ET (Sat Jun 01 2013 - 20:47:05 PDT)
- Re: [AMBER] reference group and pulled group in umbrella sampling Jason Swails (Sat Jun 01 2013 - 21:29:21 PDT)
- [AMBER] tleap and ff02pol.r1 live (Sun Jun 02 2013 - 09:59:21 PDT)
- Re: [AMBER] hbond in ptraj and cpptraj pmaj.nencki.gov.pl (Mon Jun 03 2013 - 03:12:06 PDT)
- [AMBER] ptraj error parul sharma (Mon Jun 03 2013 - 04:14:13 PDT)
- [AMBER] Cu+2 problem Fabian Glaser (Mon Jun 03 2013 - 04:40:21 PDT)
- [AMBER] prmtop for stripped down coordinates Paul Driscoll (Mon Jun 03 2013 - 05:38:17 PDT)
- [AMBER] Methylated histidine lib and frcomd files George Patargias (Mon Jun 03 2013 - 06:33:46 PDT)
- [AMBER] mmGBSA bondi/mbondi2 and force field questions psu4.uic.edu (Mon Jun 03 2013 - 09:42:26 PDT)
- [AMBER] new AmberTools13 update has error in configure2 - needs changing ET (Mon Jun 03 2013 - 11:02:23 PDT)
- [AMBER] CUDA install fails on ubuntu 12.04 using GNU compiler ET (Mon Jun 03 2013 - 13:49:03 PDT)
- [AMBER] enegy minimization with restrain Rasha Alqus (Tue Jun 04 2013 - 03:01:32 PDT)
- [AMBER] surf in cpptraj doesn't support 'stripped' trajectories? Marc van der Kamp (Tue Jun 04 2013 - 09:32:18 PDT)
- [AMBER] Potential smoothing George Tzotzos (Tue Jun 04 2013 - 09:48:21 PDT)
- Re: [AMBER] example karplus.txt file for cpptraj jcoupling command Duggan, Brendan (Tue Jun 04 2013 - 11:42:49 PDT)
- [AMBER] AmberTools 13 igb=8 CalcError: $AMBERHOME/bin/mmpbsa_py_energy failed with prmtop complex.top! psu4.uic.edu (Tue Jun 04 2013 - 14:44:48 PDT)
- [AMBER] Any tips on setting up a cluster to run amber? Josh Berryman (Wed Jun 05 2013 - 02:38:00 PDT)
- [AMBER] errors compiling Jonathan Gough (Wed Jun 05 2013 - 11:23:54 PDT)
- [AMBER] iron-sulfur parameterization venkatesh s (Wed Jun 05 2013 - 11:52:59 PDT)
- [AMBER] error energy minimization with restrain Rasha Alqus (Wed Jun 05 2013 - 11:59:22 PDT)
- [AMBER] Karplus.txt file for nucleic acid residues Indrajit Deb (Thu Jun 06 2013 - 02:02:30 PDT)
- [AMBER] solvatebox membrane Kanin Wichapong (Thu Jun 06 2013 - 02:53:40 PDT)
- [AMBER] result of molsurf calculation setyanto md (Thu Jun 06 2013 - 07:36:10 PDT)
- [AMBER] Lipid11 DMPC Kanin Wichapong (Thu Jun 06 2013 - 07:56:54 PDT)
- [AMBER] CUDA install fails due to undefined netcdf definitions Matthew Wampole (Thu Jun 06 2013 - 08:28:29 PDT)
- [AMBER] using ntt=2 on gpu Sarah Graham (Thu Jun 06 2013 - 08:43:29 PDT)
- [AMBER] MMPBSA.py Error Senthil Natesan (Thu Jun 06 2013 - 08:46:12 PDT)
- [AMBER] PM6 and PM3 me, Nancy (Thu Jun 06 2013 - 11:11:01 PDT)
- [AMBER] unable to run minimizations after new installation of amber11 Amparo Garcia Lopez (Thu Jun 06 2013 - 11:59:25 PDT)
- [AMBER] ntt=2 on gpu Sarah Graham (Thu Jun 06 2013 - 12:36:34 PDT)
- [AMBER] cpptraj diffusion ambertool13 Asmita Gupta (Fri Jun 07 2013 - 05:04:49 PDT)
- [AMBER] Help regarding Mn parameters Mallipeddi, Premalatha (Fri Jun 07 2013 - 11:07:30 PDT)
- [AMBER] MMPBSA Alanine scan terminal residues BERGY (Sat Jun 08 2013 - 23:23:48 PDT)
- [AMBER] Problem with SMD moitrayee.mbu.iisc.ernet.in (Sun Jun 09 2013 - 02:06:55 PDT)
- [AMBER] What is minimum GPU bandwidth to get AMBER to run properly? ET (Sun Jun 09 2013 - 07:46:31 PDT)
- [AMBER] How to make a specific non-bonded interaction off kurisaki (Mon Jun 10 2013 - 03:22:53 PDT)
- [AMBER] How to avoid tleap error *** Error: tl_getline(): not interactive, use stdio. kurisaki (Mon Jun 10 2013 - 05:15:04 PDT)
- [AMBER] ntt=2 on gpu Sarah Graham (Mon Jun 10 2013 - 05:26:21 PDT)
- [AMBER] Calculating harmonic potential in umbrella sampling Sajeewa Pemasinghe (Mon Jun 10 2013 - 11:25:31 PDT)
- [AMBER] counterions in md simulation Mary Varughese (Tue Jun 11 2013 - 01:27:45 PDT)
- Re: [AMBER] Error in mm_pbsa Chinh Su Tran To (Tue Jun 11 2013 - 02:09:38 PDT)
- [AMBER] parameters of ions for TIP5P water box Xioling Chuang (Tue Jun 11 2013 - 03:54:57 PDT)
- [AMBER] how does leap-prmtop calculate residues in water Jonathan Gough (Tue Jun 11 2013 - 13:13:05 PDT)
- [AMBER] nab in AmberTools13: documentation of newton() and getpdb_prm() sample Chris Moth (Tue Jun 11 2013 - 13:49:13 PDT)
- [AMBER] prmtop Bailey, Steven (Wed Jun 12 2013 - 06:42:46 PDT)
- [AMBER] csh problem Albert (Wed Jun 12 2013 - 10:44:08 PDT)
- [AMBER] Protein leaving periodic box Hailin Huang (Wed Jun 12 2013 - 13:56:58 PDT)
- [AMBER] Running MD NPT Ensemble Error Benjamin Grant (Wed Jun 12 2013 - 14:07:58 PDT)
- [AMBER] bad atom type: N3 (In MMGBSA decomp calculations) Jason Slingsby (Wed Jun 12 2013 - 15:38:29 PDT)
- [AMBER] Step by step tutorial to using Ptraj in generating DCCM #YIP YEW MUN# (Wed Jun 12 2013 - 18:22:20 PDT)
- [AMBER] Unknown redidue when using tleap Dongshan Wei (Wed Jun 12 2013 - 18:40:42 PDT)
- [AMBER] MPI Compilation problems Amber 12 on CentOS 6.2 Frank Thommen (Thu Jun 13 2013 - 01:36:43 PDT)
- [AMBER] glycame06_carbohydrate_hydrogen bond pattern Rasha Alqus (Thu Jun 13 2013 - 02:26:22 PDT)
- [AMBER] amber2accent perl script Manikanthan Bhavaraju (Thu Jun 13 2013 - 10:59:09 PDT)
- [AMBER] How to modify/add velocity entries in .inpcrd file? Yan Duan (Thu Jun 13 2013 - 15:56:52 PDT)
- [AMBER] problem with restart file in amber 11 Edward Pate (Thu Jun 13 2013 - 17:10:33 PDT)
- [AMBER] Amber to Charmm Manikanthan Bhavaraju (Thu Jun 13 2013 - 17:42:53 PDT)
- [AMBER] Questions about installing Amber 11 Changqing Yan (Fri Jun 14 2013 - 00:03:54 PDT)
- [AMBER] Questions about installation of Amber11 Changqing Yan (Fri Jun 14 2013 - 01:16:44 PDT)
- [AMBER] Building CUDA-enabled Amber11 (pmemd.cuda) * (Amber 11 only) Changqing Yan (Fri Jun 14 2013 - 02:29:18 PDT)
- [AMBER] Cannot find Sander in Amber13 Michelle Mukonyora (Fri Jun 14 2013 - 03:06:15 PDT)
- [AMBER] help 徐俊 (Fri Jun 14 2013 - 03:56:57 PDT)
- [AMBER] print forces experienced by molecule during simulation ET (Fri Jun 14 2013 - 05:22:53 PDT)
- Re: [AMBER] problem with parmchk and a big organic molecule Jason Swails (Fri Jun 14 2013 - 08:24:29 PDT)
- Re: [AMBER] Parameters for Aluminum Ion Jason Swails (Fri Jun 14 2013 - 08:42:25 PDT)
- [AMBER] Can RMSF be at least 2 times larger than RMSD? Yip Yew Mun (Fri Jun 14 2013 - 08:57:07 PDT)
- [AMBER] Difficulty compiling amber12/ambertools13 Hunter Brown (Fri Jun 14 2013 - 15:41:11 PDT)
- [AMBER] In regards to my previous question Hunter Brown (Fri Jun 14 2013 - 15:45:22 PDT)
- [AMBER] Experience with terachem and amber12 Fabrício Bracht (Fri Jun 14 2013 - 23:36:14 PDT)
- [AMBER] Is that a way to generate free energy landscapes with ptraj? Yip Yew Mun (Sat Jun 15 2013 - 06:29:38 PDT)
- [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Sat Jun 15 2013 - 20:26:12 PDT)
- [AMBER] cpptraj grid water density Asmita Gupta (Sun Jun 16 2013 - 06:01:26 PDT)
- [AMBER] selective aMD Thomas Evangelidis (Sun Jun 16 2013 - 09:43:30 PDT)
- [AMBER] How can I calculate the individual PBSA energies of a large set Changqing Yan (Sun Jun 16 2013 - 17:41:01 PDT)
- [AMBER] What bugfix.18 actually does to correct the problem in NPT simulations on GPU? Takato Sato (Mon Jun 17 2013 - 01:54:00 PDT)
- [AMBER] Assessing Antechamber temporary files Kamali Sripathi (Mon Jun 17 2013 - 05:03:11 PDT)
- [AMBER] Graphene topology from GAFF dpiraner.caltech.edu (Mon Jun 17 2013 - 11:48:48 PDT)
- [AMBER] Need a higher value for SKINNB Hailin Huang (Mon Jun 17 2013 - 15:20:57 PDT)
- [AMBER] Difficulty in reading .mdcrd file in VMD Yan Duan (Mon Jun 17 2013 - 16:07:31 PDT)
- [AMBER] qmcut in QM/MM simulation with AMBER/GAUSSIAN Tamara Meirelles (Mon Jun 17 2013 - 17:39:00 PDT)
- [AMBER] MMPBSA.py and cpptraj error Sorensen, Jesper (Mon Jun 17 2013 - 20:35:08 PDT)
- [AMBER] ERROR: GPU runs fail with nfft Error only when running 2x geforce TITANS in same machine ET (Mon Jun 17 2013 - 22:21:49 PDT)
- [AMBER] Cellulose NVE with pmemd.cuda.MPI Nakashima, Yoshihisa (Mon Jun 17 2013 - 23:19:50 PDT)
- [AMBER] hydrogen bond pattern Rasha Alqus (Tue Jun 18 2013 - 04:51:31 PDT)
- [AMBER] PEG Bailey, Steven (Tue Jun 18 2013 - 05:18:24 PDT)
- [AMBER] A and Z-DNA arnab bhattacharya (Tue Jun 18 2013 - 06:34:31 PDT)
- [AMBER] cpptraj: can we retrieve the minimal distance between two sets of residues? Jan-Philip Gehrcke (Tue Jun 18 2013 - 06:56:46 PDT)
- [AMBER] D amino acids Krisztina Feher (Tue Jun 18 2013 - 07:11:47 PDT)
- [AMBER] Job stops due to INFO: Old style inpcrd file read Aditya Padhi (Tue Jun 18 2013 - 08:32:28 PDT)
- [AMBER] RADIAL ptraj vs cpptraj Domenico Marson (Tue Jun 18 2013 - 09:42:08 PDT)
- [AMBER] Amber compile, number of files Hunter Brown (Tue Jun 18 2013 - 10:15:25 PDT)
- [AMBER] gaff atom type inhee park (Tue Jun 18 2013 - 12:39:26 PDT)
- [AMBER] tleap has error by applying amber ff03ua Chris Moth (Tue Jun 18 2013 - 15:56:25 PDT)
- [AMBER] Nonbond cells need to be recalculated, restart simulation from previous checkpoint with a higher value for skinnb. 涂志萍 (Wed Jun 19 2013 - 02:35:01 PDT)
- [AMBER] Thanks Hunter Brown (Wed Jun 19 2013 - 09:07:07 PDT)
- [AMBER] Curious behavior of cpptraj in ambertools 13.1 Fabrício Bracht (Wed Jun 19 2013 - 09:49:28 PDT)
- [AMBER] Update 10 for AmberTools 13: CPPTRAJ Daniel Roe (Wed Jun 19 2013 - 10:03:01 PDT)
- [AMBER] Experiences with GTX 780 in the framework of Amber calculations ? Marek Maly (Wed Jun 19 2013 - 10:35:58 PDT)
- [AMBER] Difficulty running sander Hunter Brown (Wed Jun 19 2013 - 11:10:35 PDT)
- [AMBER] NAB extract residue from molecule Le,Huy Tuan (Wed Jun 19 2013 - 11:31:12 PDT)
- [AMBER] Access to Quanta or CHARMM software Manikanthan Bhavaraju (Wed Jun 19 2013 - 12:33:13 PDT)
- [AMBER] receiving amber digest not separate subject wise as earlier Vaibhav Dixit (Thu Jun 20 2013 - 01:15:07 PDT)
- [AMBER] Is per atome decomposition in MM-PBSA possible? Haralambos Tzoupis (Thu Jun 20 2013 - 02:37:11 PDT)
- [AMBER] Fwd: Re: Graphene topology from GAFF FyD (Thu Jun 20 2013 - 07:02:04 PDT)
- [AMBER] GAFF atom type for CO Krisztina Feher (Thu Jun 20 2013 - 11:16:17 PDT)
- [AMBER] adding Mg2+ as Counter ion for MD simulations Pranjal Mahanta (Thu Jun 20 2013 - 11:34:30 PDT)
- [AMBER] Anyone running machines with Quad GPU setups ET (Thu Jun 20 2013 - 17:18:59 PDT)
- [AMBER] "vlimit exceeded for step" for constant surface tension simulation Wei Lin (Thu Jun 20 2013 - 18:09:32 PDT)
- [AMBER] How to define restraint for Umbrella sampling Sindrila Dutta banik (Fri Jun 21 2013 - 00:46:17 PDT)
- [AMBER] Calculating Hydrophobic Interaction Ravi Tripathi (Fri Jun 21 2013 - 05:31:24 PDT)
- [AMBER] post-clustering calculation of DBI and pSF Amparo Garcia Lopez (Fri Jun 21 2013 - 06:34:26 PDT)
- [AMBER] Troubles running LEaP Hunter Brown (Fri Jun 21 2013 - 11:57:39 PDT)
- [AMBER] Fluctuation of density during equilibration phase Ibrahim Said (Fri Jun 21 2013 - 13:23:54 PDT)
- [AMBER] inhomogeneous solvent mixture Chinthaka Ratnaweera (Fri Jun 21 2013 - 21:36:01 PDT)
- [AMBER] MMPBSA per-residue stuck forever without output even for 3 frames only M Elkot (Sat Jun 22 2013 - 07:36:53 PDT)
- [AMBER] Actual Intel Compiler Version Used Ismail, Mohd F. (Sun Jun 23 2013 - 18:47:33 PDT)
- [AMBER] error of PBSA calculation Changqing Yan (Mon Jun 24 2013 - 01:03:45 PDT)
- [AMBER] Provisional GTX780 Numbers Ross Walker (Mon Jun 24 2013 - 14:23:02 PDT)
- [AMBER] issue in tleap Rejwan (Mon Jun 24 2013 - 14:25:27 PDT)
- [AMBER] What are the controls parameters for the nmode command line tool Jose Borreguero (Mon Jun 24 2013 - 16:39:21 PDT)
- [AMBER] Questions about ncsu_smd in Amber12 moitrayee.mbu.iisc.ernet.in (Mon Jun 24 2013 - 20:51:34 PDT)
- [AMBER] MMPBSA.py problem Asmita Gupta (Tue Jun 25 2013 - 00:07:05 PDT)
- [AMBER] Fwd: Fwd: Re: Is it a bug? Compilation Error in Ambertools Matthias Bohner (Tue Jun 25 2013 - 00:40:37 PDT)
- [AMBER] PB Bomb in pb_aaradi() - missing ff12SB atom types Hannes Loeffler (Tue Jun 25 2013 - 03:05:39 PDT)
- [AMBER] Amber updater issues eneas.usal.es (Tue Jun 25 2013 - 09:04:22 PDT)
- [AMBER] Cutoff smoothing George Tzotzos (Tue Jun 25 2013 - 09:17:24 PDT)
- [AMBER] [Re:] Amber updater issues eneas.usal.es (Tue Jun 25 2013 - 09:28:09 PDT)
- [AMBER] MMPBSA.py error eneas.usal.es (Tue Jun 25 2013 - 09:37:33 PDT)
- [AMBER] Amber updater issues eneas.usal.es (Tue Jun 25 2013 - 09:58:26 PDT)
- [AMBER] Amber updater issues eneas.usal.es (Tue Jun 25 2013 - 10:25:52 PDT)
- [AMBER] entropy calculation starts from where it stops psu4.uic.edu (Tue Jun 25 2013 - 10:34:15 PDT)
- [AMBER] Questions about SMD using jar=1 moitrayee.mbu.iisc.ernet.in (Tue Jun 25 2013 - 12:23:24 PDT)
- [AMBER] unable to compile amberTools12 Christopher Neale (Tue Jun 25 2013 - 12:38:44 PDT)
- [AMBER] Custom topology parameter usage Parker de Waal (Tue Jun 25 2013 - 21:18:39 PDT)
- [AMBER] Force-field for non-native peptide containing fluoride Cheng-I Lee (Wed Jun 26 2013 - 02:14:43 PDT)
- Re: [AMBER] mmpbsa-with and without entropy colvin (Wed Jun 26 2013 - 03:19:22 PDT)
- [AMBER] GTX780 News Ross Walker (Wed Jun 26 2013 - 16:31:26 PDT)
- [AMBER] Cupper cluster parametrization with MCPB mmaestre.gate.sinica.edu.tw (Wed Jun 26 2013 - 18:42:25 PDT)
- Re: [AMBER] GTX780 Fabrício Bracht (Wed Jun 26 2013 - 19:33:32 PDT)
- [AMBER] Binding energy eneas.usal.es (Thu Jun 27 2013 - 01:26:37 PDT)
- [AMBER] TI calculations and autocorrelation time Kepa K. Burusco (Thu Jun 27 2013 - 07:56:48 PDT)
- [AMBER] Warnings in leap about lipid11 eneas.usal.es (Thu Jun 27 2013 - 08:01:54 PDT)
- [AMBER] Is there any major change of MMPBSA.py in AmberTools 13? psu4.uic.edu (Thu Jun 27 2013 - 09:02:42 PDT)
- [AMBER] FATAL: Atom XXX does not have a type sunyeping.aliyun.com (Thu Jun 27 2013 - 11:58:16 PDT)
- [AMBER] mmpbsa not included in Amber11? Changqing Yan (Thu Jun 27 2013 - 19:55:27 PDT)
- [AMBER] energy analysis in amber Asmita Gupta (Thu Jun 27 2013 - 23:11:08 PDT)
- [AMBER] How to define reaction coordinate in Umbrella sampeling Sindrila Dutta banik (Fri Jun 28 2013 - 00:42:08 PDT)
- [AMBER] Problem with PDB files in LEaP Hunter Brown (Fri Jun 28 2013 - 08:09:58 PDT)
- [AMBER] 回复：Re: FATAL: Atom XXX does not have a type sunyeping.aliyun.com (Fri Jun 28 2013 - 09:05:16 PDT)
- Re: [AMBER] Problematic PDB files Daniel Roe (Fri Jun 28 2013 - 12:35:43 PDT)
- [AMBER] avgcoord in AT13 Hongyi WU (Fri Jun 28 2013 - 12:51:19 PDT)
- [AMBER] How to get correlation matrix of center of mass of partial atoms for residues? Baogen Duan (Fri Jun 28 2013 - 23:44:28 PDT)
- [AMBER] problem with MM-PBSA Maryam Hamzehee (Sat Jun 29 2013 - 08:27:49 PDT)
- [AMBER] error in running MMPBSA.MPI onetwo (Sun Jun 30 2013 - 07:50:28 PDT)
- Last message date: Sun Jun 30 2013 - 08:00:02 PDT
- Archived on: Fri Apr 19 2024 - 05:54:34 PDT
