Amber Archive Nov 2016 by messages with attachments

[AMBER] Problem with bonds in NAB Vladislav Sláma (Wed Nov 02 2016 - 08:39:12 PDT)
1. nmode.nab (795 bytes)
2. run.sh (220 bytes)
3. 5hex_Reparam.prmtop (252957 bytes)
4. 5hex_Reparam.inpcrd (12057 bytes)
5. 5hex_Reparam.pdb (22124 bytes)
6. 5hex_Reparam.mol2 (34178 bytes)
7. 5hex_Reparam.frcmod (3903 bytes)
8. 01_Min.in (135 bytes)
9. tleap.in (244 bytes)
[AMBER] Uridine diphosphate (UDP) - tleap Anna Cebrian Prats (Fri Nov 04 2016 - 04:58:51 PDT)
1. ligand.pdb (4981 bytes)
Re: [AMBER] Ligand across membrane zoran matovic (Sun Nov 06 2016 - 23:38:25 PST)
1. area_per_lipid.jpg (99843 bytes)
2. electron_density.jpg (113789 bytes)
3. 4908.png (487764 bytes)
4. 05_Prod.in (345 bytes)
[AMBER] Problem with Parmed-generated chamber prmtop Marc van der Kamp (Thu Nov 10 2016 - 07:01:48 PST)
1. fad_distorted.png (131790 bytes)
2. Parmed-Test.tar.gz (388317 bytes)
3. min_namd.pdb (6711 bytes)
4. min_test.pdb (6839 bytes)
[AMBER] GIST: convergence of the translational entropy term Sergey Samsonov (Fri Nov 11 2016 - 06:28:26 PST)
1. TS_translational_example.png (16508 bytes)
[AMBER] dlpc membrane jojartb.jgypk.u-szeged.hu (Mon Nov 14 2016 - 01:45:03 PST)
1. 2sendambermailinglist.tar.gz (685873 bytes)
Re: [AMBER] dlpc membrane jojartb.jgypk.u-szeged.hu (Mon Nov 14 2016 - 08:41:16 PST)
1. dlpc.tleap.in (196 bytes)
2. lipid.pdb (8161 bytes)
3. leap.zip (31152 bytes)
Re: [AMBER] Negative interaction energy between Sodium ions? Oliver Emil Skytte Glue (Mon Nov 14 2016 - 14:29:17 PST)
1. _DNA__Ions.png (100663 bytes)
Re: [AMBER] Umbrella simulation with an arbitrary bias potential diego.soler.uam.es (Tue Nov 15 2016 - 02:53:15 PST)
1. free_energy.dat (55863 bytes)
[AMBER] Converting coordinate file generated into pdb format for nuparm ABHIJEET CHOWDHURY (Thu Nov 17 2016 - 04:43:59 PST)
1. pdbout.999 (94139 bytes)
2. traj_pdb.in (715 bytes)
[AMBER] Issue with addAtomType: Syntax Error Korey M Reid (Thu Nov 17 2016 - 12:14:36 PST)
1. frcmod.hemall (2947 bytes)
2. heme_all.in (7924 bytes)
3. hemeprot.pdb (201618 bytes)
4. leap_addatomtype_issue.log (17716 bytes)
Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) The Cromicus Productions (Fri Nov 18 2016 - 16:29:10 PST)
1. my_file.py (340 bytes)
2. nuc.pdb (51199 bytes)
3. v00.dat (16262 bytes)
Re: [AMBER] Convert prm into prmtop - from NAMD to AMBER The Cromicus Productions (Mon Nov 21 2016 - 11:36:27 PST)
1. sequence.pdb (50492 bytes)
2. sequence.rst (23298 bytes)
[AMBER] Protein path error Arthi Venkat (Tue Nov 22 2016 - 01:52:18 PST)
1. amber_error.png (128473 bytes)
[AMBER] rmsf problem Sepideh Jafari (Wed Nov 23 2016 - 02:07:27 PST)
1. rmsf.png (53565 bytes)
2. rmsd.png (50230 bytes)
[AMBER] more on the Berendsen thermostat David A Case (Wed Nov 23 2016 - 10:44:29 PST)
1. rms.pdf (111719 bytes)
Re: [AMBER] Problem with bonds in NAB Vladislav Sláma (Thu Nov 24 2016 - 06:58:16 PST)
1. 5hex_esp-charges-ini.esp (475690 bytes)
2. tleap.in (196 bytes)
3. nmode.nab (771 bytes)
4. 01_Min.in (135 bytes)
5. run.sh (366 bytes)
6. Min-Structure.png (48056 bytes)
7. Min-Structure.png (42352 bytes)
[AMBER] GlcNAc-UDP problem with frcmod file Sonia Romero (Fri Nov 25 2016 - 02:15:41 PST)
1. UGN_mod_leap.mol2 (6215 bytes)
2. UGN_mod_attype_mod.prep (4906 bytes)
[AMBER] Fw: Problems with imaging Mark Waterhouse [RPG] (Mon Nov 28 2016 - 12:49:09 PST)
1. image001.png (20971 bytes)
Re: [AMBER] Fw: Problems with imaging Mark Waterhouse [RPG] (Wed Nov 30 2016 - 01:08:00 PST)
1. Distance2.PNG (92820 bytes)
[AMBER] Issue with the gaff parameters for "nh" atom type Prajwal Nandekar (Wed Nov 30 2016 - 05:58:45 PST)
1. nadp_gaff_issue.jpg (59467 bytes)

Last message date: Wed Nov 30 2016 - 16:00:03 PST
Archived on: Mon Nov 25 2024 - 05:55:20 PST

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