Amber Archive Jun 2017: by messages with attachments

[AMBER] Error during the installion Jeyaram R A (Thu Jun 01 2017 - 05:25:29 PDT)
1. file_1.png (222663 bytes)
Re: [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial Nikolay N. Kuzmich (Thu Jun 01 2017 - 09:50:28 PDT)
1. Sustiva_xleap2.png (18753 bytes)
2. Sustiva_xleap.png (49926 bytes)
[AMBER] TI free energy calculation errors Sumudu Leelananda (Thu Jun 01 2017 - 11:16:38 PDT)
1. rest_step1.in (633 bytes)
2. step1_heat0.in (459 bytes)
3. step1_heat1.in (497 bytes)
4. step1_min0.in (355 bytes)
5. step1_min1.in (393 bytes)
6. step1_md0.in (562 bytes)
7. step1_md1.in (600 bytes)
8. 1AP4_protein_1CA6.pdb (112334 bytes)
9. TI_step1_lambda_03.pbs (1629 bytes)
Re: [AMBER] TI MD simulation Sowmya Indrakumar (Fri Jun 02 2017 - 03:57:33 PDT)
1. 06-02_12-46-42.png (239449 bytes)
[AMBER] average no. of H bond between ligand-solvent. Saman Yousuf ali (Tue Jun 06 2017 - 05:02:31 PDT)
1. sample.png (93308 bytes)
[AMBER] Regarding empty lig.frcmod file Vishal Nemaysh (Tue Jun 06 2017 - 09:27:45 PDT)
1. lig.frcmod (62 bytes)
2. lig.mol2 (3617 bytes)
3. lig.pdb (2907 bytes)
4. lig.prepin (3026 bytes)
5. NEWPDB.PDB (2275 bytes)
6. PREP.INF (4349 bytes)
7. Protein_Ligend.pdb (193234 bytes)
8. sqm.in (2019 bytes)
9. sqm.out (10656 bytes)
10. sqm.pdb (1925 bytes)
[AMBER] Velocity autocorrelation ATUL KUMAR (Wed Jun 07 2017 - 04:22:37 PDT)
1. vel_auto_cor.out (650027 bytes)
Re: [AMBER] PCA analysis Thakur, Abhishek (Thu Jun 08 2017 - 11:33:58 PDT)
1. pca.out (3233 bytes)
2. pca.trajin (1173 bytes)
[AMBER] SASA calculation Garima Singh (Thu Jun 08 2017 - 22:40:05 PDT)
1. 06-09_11:05:59.png (187188 bytes)
Re: [AMBER] Regarding empty lig.frcmod file Vishal Nemaysh (Fri Jun 09 2017 - 05:45:54 PDT)
1. lig.mol2 (3617 bytes)
Re: [AMBER] Regarding empty lig.frcmod file Elvis Martis (Fri Jun 09 2017 - 06:06:38 PDT)
1. lig.mol2 (3620 bytes)
[AMBER] Fwd: SASA calculation Garima Singh (Mon Jun 12 2017 - 00:07:13 PDT)
1. sasa.dat (550000 bytes)
2. 06-12_12:30:22.png (123405 bytes)
[AMBER] mdgx extracting energies Charles-Alexandre Mattelaer (Mon Jun 12 2017 - 06:36:27 PDT)
1. 04_ExtractEnergies (109 bytes)
2. energies_mdgx.dat (7701 bytes)
3. energies_sed.dat (22197 bytes)
4. Conf1.oout (80428 bytes)
Re: [AMBER] RNA parameters for wc_helix Supriyo Naskar (Mon Jun 12 2017 - 07:10:02 PDT)
1. wc_dna.nab (196 bytes)
2. out.out (3695 bytes)
[AMBER] Fwd: test serial amber 14 and ambertool15 co nguyentruong (Wed Jun 14 2017 - 07:58:38 PDT)
1. 06-14_15-40-48.diff (12948 bytes)
Re: [AMBER] problem regarding ACE capping of the protein terminal of the PDB Saikat Pal (Thu Jun 15 2017 - 03:38:27 PDT)
1. leap-1.pdb (373948 bytes)
2. new.pdb (223163 bytes)
Re: [AMBER] How to solve the unfilled valence problem in antechamber Ashish Radadiya (Thu Jun 15 2017 - 06:23:31 PDT)
1. isg.mol2 (1830 bytes)
2. isg_aromatic.ac (1874 bytes)
3. isg_singleDouble.ac (1874 bytes)
Re: [AMBER] Regarding empty lig.frcmod file Vishal Nemaysh (Fri Jun 16 2017 - 05:44:10 PDT)
1. lig.pdb (2907 bytes)
Re: [AMBER] How to solve the unfilled valence problem in antechamber Ashish Radadiya (Fri Jun 16 2017 - 11:17:58 PDT)
1. isg_singleDouble.ac (1874 bytes)
[AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes Maryam Hamzehee (Wed Jun 21 2017 - 02:23:10 PDT)
1. equil.out (3082 bytes)
[AMBER] issue in antechamber17 bcc charges with mopac Alessandro Contini (Wed Jun 21 2017 - 04:48:17 PDT)
1. charge_tests.tar.bz2 (55205 bytes)
[AMBER] Leap: Periodic Boundary of DNA Johannes Kalliauer (Wed Jun 21 2017 - 06:44:45 PDT)
1. nuc10.pdb (51848 bytes)
2. LeapVorbereitung.leap (232 bytes)
3. tleapDNA.log (4294 bytes)
[AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time SHAILESH KUMAR (Thu Jun 22 2017 - 06:51:00 PDT)
1. vmdscene2.pdf (222717 bytes)
Re: [AMBER] TI free energy calculation errors Sumudu Leelananda (Wed Jun 28 2017 - 09:18:26 PDT)
1. sander_june_28.zip (14261 bytes)
Re: [AMBER] sander do not write rst and mdcrd files Rana Rehan Khalid (Wed Jun 28 2017 - 10:49:53 PDT)
1. 06-28_13-31-14.png (124462 bytes)
Re: [AMBER] sander do not write rst and mdcrd files Rana Rehan Khalid (Wed Jun 28 2017 - 11:04:55 PDT)
1. 06-28_14-02-28.png (122626 bytes)
Re: [AMBER] TI free energy calculation errors Sumudu Leelananda (Wed Jun 28 2017 - 12:05:13 PDT)
1. rest_step2.in (1221 bytes)
2. step2_heat0.in (497 bytes)
3. step2_md0.in (617 bytes)
4. step2_heat1.in (515 bytes)
5. step2_min1.in (411 bytes)
6. step2_min0.in (393 bytes)
7. step2_min0.out (4880 bytes)
8. step2_heat0.out (4162 bytes)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Wed Jun 28 2017 - 15:34:13 PDT)
1. leap.log (59833 bytes)
[AMBER] antechamber Rana Rehan Khalid (Wed Jun 28 2017 - 15:37:12 PDT)
1. leap.log (59833 bytes)
Re: [AMBER] antechamber Rana Rehan Khalid (Wed Jun 28 2017 - 21:56:59 PDT)
1. leap.log (4464 bytes)
2. hem.pdb (3563 bytes)
Re: [AMBER] antechamber Rana Rehan Khalid (Wed Jun 28 2017 - 23:07:18 PDT)
1. heme_all.in (7009 bytes)
2. heme.frcmod (3321 bytes)
Re: [AMBER] antechamber Elvis Martis (Wed Jun 28 2017 - 23:16:20 PDT)
1. heme.frcmod (2920 bytes)
[AMBER] constant pH MD question Michael Shokhen (Thu Jun 29 2017 - 02:17:58 PDT)
1. Picture1.jpg (9592 bytes)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Thu Jun 29 2017 - 12:05:31 PDT)
1. hem.pdb (3563 bytes)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Thu Jun 29 2017 - 20:09:31 PDT)
1. leap.log (3322 bytes)

Amber Archive Jun 2017 by messages with attachments