Amber Archive Nov 2017: by messages with attachments

[AMBER] MCPB.py step 1 help please Eugene Cha (Wed Nov 01 2017 - 12:14:31 PDT)
1. Cu_GGH.zip (2624 bytes)
[AMBER] How to generate inpcrd and prmtop files for A and B mixed solution 杨满意 (Wed Nov 01 2017 - 18:52:38 PDT)
1. a1.frcmod (725 bytes)
2. a1.mol2 (4099 bytes)
3. a1.pdb (2050 bytes)
4. a1_a.frcmod (725 bytes)
5. a1_a.mol2 (2533 bytes)
6. a1_a.pdb (1225 bytes)
7. a1_b.frcmod (62 bytes)
8. a1_b.mol2 (1743 bytes)
9. a1_b.pdb (840 bytes)
10. tleap1.in (307 bytes)
11. tleap2.in (515 bytes)
Re: [AMBER] Acetate ion using xleap Shilpa Gupta (Thu Nov 02 2017 - 22:11:52 PDT)
1. ace.mol2 (846 bytes)
[AMBER] error: Atom does not have type Shilpa Gupta (Tue Nov 07 2017 - 23:32:57 PST)
1. leap.log (51325 bytes)
[AMBER] No torsion terms error even though I specified them in frcmod file Adebayo Adeniyi (Wed Nov 08 2017 - 03:10:05 PST)
1. dna.frcmod (3514 bytes)
[AMBER] Amber GCC 6.4.0 and MKL 2017.3.196 build failing Joachim Hein (Fri Nov 10 2017 - 08:32:36 PST)
1. 11-10_at_17.27.14.png (119093 bytes)
Re: [AMBER] Amber GCC 6.4.0 and MKL 2017.3.196 build failing Joachim Hein (Fri Nov 10 2017 - 08:35:14 PST)
1. 11-10_at_17.33.25.png (125039 bytes)
Re: [AMBER] Running Explicit pH MD Pacheco, Sayuri (Fri Nov 10 2017 - 10:56:28 PST)
1. HdeA_Exp_pH_step1_mini.in (278 bytes)
2. HdeA_Exp_pH_step2_heat.in (315 bytes)
3. HdeA_Exp_pH_step4_prod.in (289 bytes)
4. HdeA_Exp_pH_step3_equi.in (387 bytes)
[AMBER] error of pdb4amber jacky zhao (Sun Nov 12 2017 - 08:03:39 PST)
1. 11-12_______11.55.17.png (125222 bytes)
Re: [AMBER] error of pdb4amber jacky zhao (Sun Nov 12 2017 - 13:51:19 PST)
1. HAC1.pdb (257866 bytes)
[AMBER] the CYX problem of generation parm7 crd files by AT17 jacky zhao (Sun Nov 12 2017 - 15:14:49 PST)
1. 11-13_______7.09.18.png (173730 bytes)
2. HAC1_for_simulation.pdb (261037 bytes)
[AMBER] error of pdb4amber Lei Zhao (Sun Nov 12 2017 - 08:02:59 PST)
1. 11-12_______11.55.17.png (125222 bytes)
[AMBER] Regarding Glucose dynamics Aashish Bhatt (Tue Nov 14 2017 - 06:48:06 PST)
1. Capture11.PNG (13183 bytes)
2. Capture22.PNG (16500 bytes)
Re: [AMBER] Regarding Glucose dynamics Lachele Foley (Tue Nov 14 2017 - 08:16:26 PST)
1. vmdscene.dat.png (59033 bytes)
[AMBER] The strange way of paramfit working process viktor drobot (Tue Nov 14 2017 - 13:32:33 PST)
1. ______________________.png (41461 bytes)
2. ______________________.png (55073 bytes)
3. 11-15_00-00-37.png (2178 bytes)
[AMBER] Distorted peptide Chetna Tyagi (Thu Nov 16 2017 - 07:12:27 PST)
1. image.png (49476 bytes)
[AMBER] Equilibration sara.iti.lk (Sun Nov 19 2017 - 22:20:22 PST)
1. all.jpeg (32519 bytes)
[AMBER] Query about the Glucose Parameters Aashish Bhatt (Mon Nov 20 2017 - 04:00:08 PST)
1. 0ga.txt (3893 bytes)
2. glc_mk.txt (3868 bytes)
3. glc_resp.txt (3893 bytes)
4. 0ga.PNG (24452 bytes)
Re: [AMBER] Equilibration sara.iti.lk (Wed Nov 22 2017 - 22:30:54 PST)
1. rmsd_fluctuations.png (46713 bytes)
2. ACE.png (422430 bytes)
Re: [AMBER] Query about the Glucose Parameters Aashish Bhatt (Thu Nov 23 2017 - 21:48:32 PST)
1. OH_bond.png (19421 bytes)
[AMBER] Regarding Resp charge Aashish Bhatt (Sat Nov 25 2017 - 06:18:09 PST)
1. linker_resp.respin1 (544 bytes)
Re: [AMBER] PCA eigenvalues Elvis Martis (Mon Nov 27 2017 - 04:05:47 PST)
1. pca.in (1188 bytes)
Re: [AMBER] PCA eigenvalues Marcelo Andrade Chagas (Mon Nov 27 2017 - 07:52:09 PST)
1. cpu-gpu.cpptraj (6506 bytes)
2. COMANDOS-PCA-II (3492 bytes)
3. tira.cpptraj (95 bytes)
4. PCA.cpptraj (93 bytes)
5. media.cpptraj (62 bytes)
Re: [AMBER] PCA eigenvalues Nisha Amarnath Jonniya (Tue Nov 28 2017 - 00:40:59 PST)
1. pca_5drb.eps (37782 bytes)
[AMBER] APR error Maura Malinska (Tue Nov 28 2017 - 03:25:14 PST)
1. apr.in.txt (4521 bytes)
[AMBER] Using soft-core potentials to run TI simulations Yang Jinpeng (Wed Nov 29 2017 - 02:50:12 PST)
1. Catch.jpg (60466 bytes)
2. CatchAB46.jpg (71525 bytes)
Re: [AMBER] PCA eigenvalues Nisha Amarnath Jonniya (Wed Nov 29 2017 - 03:24:50 PST)
1. pca.eps (376054 bytes)
[AMBER] imin=5 not working in AMBER16? Paul Mortenson (Wed Nov 29 2017 - 07:19:37 PST)
1. imin5.tgz (474874 bytes)
Re: [AMBER] imin=5 not working in AMBER16? Paul Mortenson (Wed Nov 29 2017 - 23:52:08 PST)
1. imin5_netcdf.tgz (581125 bytes)
[AMBER] MCPB.py how to insert the heteroatom heme in the one domain of macromolecule Rana Rehan Khalid (Thu Nov 30 2017 - 06:44:54 PST)
1. imageee.png (371080 bytes)

Amber Archive Nov 2017 by messages with attachments