Amber Archive May 2017: by messages with attachments

Re: [AMBER] [SPAM] Re: consult about LEaP in amber 张壮壮 (Mon May 01 2017 - 07:28:07 PDT)
1. RNA_amber.rar (597509 bytes)
Re: [AMBER] Too many iterations in routine! in RMSD calculation kungking Hanpaibool (Mon May 01 2017 - 08:50:42 PDT)
1. rmsd_cpptraj_ch.out (541812 bytes)
[AMBER] acdoctor: fatal error when reading carboxylates from .mol2 files Niel Henriksen (Mon May 01 2017 - 15:09:32 PDT)
1. but.pdb (1136 bytes)
[AMBER] Fwd: failed to generate parameter and topology file for protein-ligand complex containing zinc Sharon D. Morris (Tue May 02 2017 - 05:22:55 PDT)
1. leap_2.log (24176 bytes)
[AMBER] Regarding amber-gaussian QM/MM problem Budhathoki, Dipesh (Tue May 02 2017 - 15:35:08 PDT)
1. amber_gauss_testing_min.out (12894 bytes)
2. gau_job.log (124183 bytes)
[AMBER] LEaP failing after update to AmberTools17 Charles-Alexandre Mattelaer (Wed May 03 2017 - 10:35:19 PDT)
1. leap.log (13970 bytes)
Re: [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber. Daniel Roe (Fri May 05 2017 - 11:29:08 PDT)
1. cpptraj.ligand.parm7 (77520 bytes)
[AMBER] Cpptraj calculates only three PHI-PSI angles in a 18-residue long peptide Chetna Tyagi (Mon May 08 2017 - 08:07:34 PDT)
1. pep.pdb (21010 bytes)
2. PEPOL.prmtop (127736 bytes)
[AMBER] how to draw Radial Distribution Functions? Yang Jinpeng (Wed May 10 2017 - 05:15:30 PDT)
1. InsertPic_.png (8745 bytes)
[AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin') Ramin Salimi (Sat May 13 2017 - 05:21:35 PDT)
1. length40.prmtop (331138 bytes)
Re: [AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin') Elvis Martis (Sat May 13 2017 - 06:17:22 PDT)
1. heat.in (253 bytes)
Re: [AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin') Elvis Martis (Sat May 13 2017 - 06:21:00 PDT)
1. heat.in (254 bytes)
[AMBER] dimer rmsd issue. Saman Yousuf ali (Sun May 14 2017 - 10:13:54 PDT)
1. rmsd.png (30727 bytes)
[AMBER] NetCDF error: Invalid argument xu qingliang (Sat May 20 2017 - 06:03:18 PDT)
1. attachment.zip (18975 bytes)
Re: [AMBER] Error while upgrading to AmberTools 17 Chetna Tyagi (Thu May 25 2017 - 04:15:11 PDT)
1. main.py (32765 bytes)
[AMBER] add ligand parameters Loris Moretti (Fri May 26 2017 - 01:45:01 PDT)
1. leap (197 bytes)
2. system_md.cdf (15968 bytes)
3. system_init.crd (413 bytes)
4. system_init.prm (12455 bytes)
5. ligand.frcmod (675 bytes)
6. ligand.mol2 (1342 bytes)
7. md.in (179 bytes)
Re: [AMBER] add ligand parameters Loris Moretti (Fri May 26 2017 - 03:19:32 PDT)
1. system_init.png (79036 bytes)
2. system_min.png (72217 bytes)
[AMBER] Question about RMSD "jumps" Ly, Thu Ngoc Anh (Sat May 27 2017 - 16:26:55 PDT)
1. RMSDs.png (57604 bytes)
Re: [AMBER] KeyError: 'A' (MCPB.py) Sushi Shilpa (Tue May 30 2017 - 21:15:34 PDT)
1. ArsD_small.pdb (1650 bytes)
Re: [AMBER] amino-cyclopropyl parameters Loris Moretti (Wed May 31 2017 - 00:32:48 PDT)
1. aminocyclopropyl.pdb (873 bytes)
Re: [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial Nikolay N. Kuzmich (Wed May 31 2017 - 04:43:20 PDT)
1. sqm.out (10579 bytes)
2. sqm_nick.out (11128 bytes)
3. sustiva_nick.mol2 (3190 bytes)
4. sustiva.mol2.save (3190 bytes)
Re: [AMBER] amino-cyclopropyl parameters David A Case (Wed May 31 2017 - 05:20:21 PDT)
1. aminocyclopropyl.pdb (874 bytes)

Amber Archive May 2017 by messages with attachments