Amber Archive Apr 2016: by messages with attachments

[AMBER] aMD ruins membrane structure Michael Shokhen (Fri Apr 01 2016 - 01:03:06 PDT)
1. pastedImage.png (565212 bytes)
Re: [AMBER] hoogsteen base pair Martina Devi (Fri Apr 01 2016 - 08:25:28 PDT)
1. b.pdb (5435 bytes)
[AMBER] turning of non-bonded interactions with addExclusions Batuhan Kav (Mon Apr 04 2016 - 02:42:30 PDT)
1. new.prmtop (110371 bytes)
2. original.prmtop (71294 bytes)
Re: [AMBER] Amber: .rst file not created ABHIJEET CHOWDHURY (Thu Apr 07 2016 - 04:47:27 PDT)
1. mi_eq14.out (16709 bytes)
Re: [AMBER] How to prepare files cyclodextrin to use witch glycam04 CRISTIAN ROSSI PERARO (Fri Apr 08 2016 - 20:32:49 PDT)
1. 1.pdb (8093 bytes)
[AMBER] mm_pbsa.pl, that I'm doing this right? CRISTIAN ROSSI PERARO (Sun Apr 10 2016 - 11:17:32 PDT)
1. WORKING___extract_coords.mmpbsa (5089 bytes)
2. 1.png (78282 bytes)
3. 2.png (115345 bytes)
4. snapshot_statistics.out (561 bytes)
5. vacuo.prmtop (34352 bytes)
6. WORKING___binding_energy.mmpbsa (8374 bytes)
[AMBER] Could not find angle parameter Jesmita Dhar (Mon Apr 11 2016 - 02:32:32 PDT)
1. sm_m1-c1.mol2 (39439 bytes)
2. gobig.molecule (19947 bytes)
Re: [AMBER] RMSD graph for protein-RNA complex Sreemol G (Mon Apr 11 2016 - 22:07:55 PDT)
1. 04-12_10-25-00.jpg (77861 bytes)
Re: [AMBER] Could not find angle parameter David A Case (Wed Apr 13 2016 - 05:34:49 PDT)
1. frcmod.dac (16126 bytes)
[AMBER] mm_pbsa.pl ERROR yhzahsc (Thu Apr 14 2016 - 00:42:02 PDT)
1. binding_energy.mmpbsa (11480 bytes)
2. binding_energy.log (3174 bytes)
[AMBER] hbond analysis of phosphotyrosine Wu Xu (Thu Apr 14 2016 - 19:55:56 PDT)
1. analyse_hbond_1.out (8175 bytes)
2. analyse_hbond_1.ptraj (1615 bytes)
[AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file Shreeramesh (Fri Apr 15 2016 - 04:27:48 PDT)
1. rec.pdb (70178 bytes)
2. tleap.all (475 bytes)
[AMBER] Conversion of CHARMM-GUI generated file into Lipid14 readable file Shreeramesh (Fri Apr 15 2016 - 05:01:04 PDT)
1. rec.pdb (70178 bytes)
2. tleap.all (475 bytes)
[AMBER] mpi problems Gard Nelson (Mon Apr 18 2016 - 11:46:06 PDT)
1. 04-14_18-24-02.log (219471 bytes)
[AMBER] Regarding atom types Elvis Martis (Tue Apr 19 2016 - 21:56:47 PDT)
1. sander_com.64.out (8079 bytes)
Re: [AMBER] Building Cyclic Peptide in xleap Kenneth McGuinness (Fri Apr 22 2016 - 09:43:36 PDT)
1. cff.pdb (4475 bytes)
[AMBER] Energies in QM/MM MD 王美婷 (Mon Apr 25 2016 - 01:46:48 PDT)
1. imin_5.in (377 bytes)
2. qmmm_md.in (413 bytes)
[AMBER] Error while converting CHARMM-GUI generated file Shreeramesh (Mon Apr 25 2016 - 05:17:08 PDT)
1. Archive.zip (497212 bytes)
Re: [AMBER] Read/visualize volmap output (opendx) Jean-Patrick Francoia (Mon Apr 25 2016 - 12:26:08 PDT)
1. test_volmap.dx (1030004 bytes)
[AMBER] Problem in calculating auto time correlation function with ptraj Saheb Dutta (Wed Apr 27 2016 - 08:32:55 PDT)
1. figure.doc (344576 bytes)
Re: [AMBER] No torsion terms for CB-N*-CR-H5 Prayagraj Fandilolu (Wed Apr 27 2016 - 23:29:11 PDT)
1. trna3.log (144956 bytes)
[AMBER] tleap - protein + ligand + heme group Anna Cebrian Prats (Thu Apr 28 2016 - 08:52:13 PDT)
1. FE_3.frcmod (4565 bytes)
2. FE_3.mol2 (7256 bytes)
3. acd.frcmod (2709 bytes)
4. acd.in (4405 bytes)
5. new.pdb (364180 bytes)
[AMBER] Targeted MD error Shukla, Saurabh (Thu Apr 28 2016 - 09:46:03 PDT)
1. tmd.in (484 bytes)
Re: [AMBER] tleap - protein + ligand + heme group Anna Cebrian Prats (Fri Apr 29 2016 - 08:16:21 PDT)
1. frcmod.hemall (3163 bytes)
2. heme_all.in (7012 bytes)
Re: [AMBER] ambpdb error Daniel Roe (Fri Apr 29 2016 - 09:17:28 PDT)
1. fixed.complex_crd.crd.gz (55402 bytes)
Re: [AMBER] tleap - protein + ligand + heme group David A Case (Fri Apr 29 2016 - 09:27:28 PDT)
1. frcmod.hemall (2845 bytes)

Amber Archive Apr 2016 by messages with attachments