Amber Archive Apr 2020: by messages with attachments

Re: [AMBER] Abasic Site and Leap Polymerization Christina Bergonzo (Sat Apr 04 2020 - 09:42:11 PDT)
1. test.ABB.pdb (50137 bytes)
2. test.pdb (60046 bytes)
Re: [AMBER] Abasic Site and Leap Polymerization Robert Molt (Sat Apr 04 2020 - 13:01:13 PDT)
1. bi6024269.pdf (591576 bytes)
[AMBER] Ligand leaving binding site at high lambdas using TI softcore Juraj Dobias (Wed Apr 08 2020 - 13:39:52 PDT)
1. equil1.in (599 bytes)
2. equil2.in (599 bytes)
3. equil3.in (753 bytes)
4. equil4.in (752 bytes)
5. heat.in (750 bytes)
6. min.in (336 bytes)
7. prod.in (522 bytes)
[AMBER] questions about paramfit ttz (Thu Apr 09 2020 - 21:54:12 PDT)
1. 5_mem_ring.prmtop (19336 bytes)
2. cft_all_structures.mdcrd (70088 bytes)
3. fit_output_ene.dat2 (6293 bytes)
4. initil_fit.out (25867 bytes)
5. job.fit.in (598 bytes)
6. sorted_ene.dat (2035 bytes)
[AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? Erdem Yeler (Fri Apr 10 2020 - 16:01:59 PDT)
1. image.png (49104 bytes)
Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests Cong Liu (Sat Apr 11 2020 - 07:25:07 PDT)
1. 04-11_at_10.22.57.png (69304 bytes)
[AMBER] geometry of amino Song Hu (Mon Apr 13 2020 - 22:59:00 PDT)
1. image003.png (3972 bytes)
2. image006.jpg (8710 bytes)
Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests Cong Liu (Tue Apr 14 2020 - 08:24:37 PDT)
1. 04-11_at_10.22.57.png (69304 bytes)
Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests Cong Liu (Tue Apr 14 2020 - 11:04:08 PDT)
1. 04-11_at_10.22.57.png (69304 bytes)
Re: [AMBER] Can I use paramfit for MM scan? Erdem Yeler (Wed Apr 15 2020 - 14:26:08 PDT)
1. image.png (10213 bytes)
2. x.inpcrd (598 bytes)
3. x.prmtop (12618 bytes)
Re: [AMBER] Interaction of cellulose-hemicellulose Pinky Mazumder (Thu Apr 16 2020 - 22:58:54 PDT)
1. 04-17_00-50-31.png (272771 bytes)
Re: [AMBER] Interaction of cellulose-hemicellulose Pinky Mazumder (Fri Apr 17 2020 - 00:45:28 PDT)
1. hema.pdb (21580 bytes)
2. cell.pdb (20986 bytes)
Re: [AMBER] Interaction of cellulose-hemicellulose Pinky Mazumder (Sun Apr 19 2020 - 22:05:17 PDT)
1. after_loaded_it_xleap.PNG (7942 bytes)
2. converted_hemi_vmd.PNG (77051 bytes)
Re: [AMBER] Interaction of cellulose-hemicellulose Lachele Foley (Sun Apr 19 2020 - 23:48:13 PDT)
1. hema_TER.pdb (21588 bytes)
Re: [AMBER] Interaction of cellulose-hemicellulose Pinky Mazumder (Mon Apr 20 2020 - 18:30:07 PDT)
1. check_hema.PNG (5402 bytes)
[AMBER] Problem in calculating pairwise interaction with CPPTRAJ Prathit Chatterjee (Tue Apr 21 2020 - 02:47:42 PDT)
1. image.png (278756 bytes)
2. image.png (291926 bytes)
[AMBER] Restraint on certain atoms during MD Debarati DasGupta (Tue Apr 21 2020 - 05:45:15 PDT)
1. 7FE26FD78D404D799A14AED71EA08EDA.png (38552 bytes)
Re: [AMBER] Restraint on certain atoms during MD Debarati DasGupta (Wed Apr 22 2020 - 15:22:03 PDT)
1. 6CF73A15FE1A4E99B37D565E1272ECC0.png (7772 bytes)
Re: [AMBER] Restraint on certain atoms during MD Debarati DasGupta (Wed Apr 22 2020 - 15:10:04 PDT)
1. FD3FE68B931D4AB7931C5BF120EC2401.png (67704 bytes)
[AMBER] Fwd: FATAL: allocation failure in ivector() error while running 3D-RISM calculations Leena Aggarwal (Thu Apr 23 2020 - 11:25:47 PDT)
1. script.sh (143 bytes)
2. tleap.pdb (286 bytes)
3. water.parm7 (8504 bytes)
4. 04-23_18:48:45.png (92503 bytes)
5. 04-23_18:48:51.png (103787 bytes)
[AMBER] wrong geometry amide nitrogen Arnaud Bondon (Fri Apr 24 2020 - 06:56:37 PDT)
1. NamidePyr.png (67982 bytes)
[AMBER] minimizing a pyridine in water Debarati DasGupta (Sat Apr 25 2020 - 06:10:52 PDT)
1. 27F9FCD505C24E35968C23E69DBC290B.png (23149 bytes)
[AMBER] Ligand lose planarity Jenny 148 (Sat Apr 25 2020 - 08:09:45 PDT)
1. nnnnn.PNG (33314 bytes)
Re: [AMBER] minimizing a pyridine in water Debarati DasGupta (Sat Apr 25 2020 - 08:38:29 PDT)
1. 3773FE3BF4C54F60BCB59D486053AC12.png (7058 bytes)
2. 7227E9CEB21B4408A03381096B88A082.png (9499 bytes)
[AMBER] Recurring problem: Ligand lose planarity Jenny 148 (Sat Apr 25 2020 - 21:49:45 PDT)
1. nnnnn.PNG (33314 bytes)
Re: [AMBER] Interaction of cellulose-hemicellulose Pinky Mazumder (Sun Apr 26 2020 - 20:59:07 PDT)
1. li.PNG (114911 bytes)
2. cell_hem_interaction.PNG (81497 bytes)
[AMBER] AMBER leap issues constructing non-standard residue Siddharth marwaha (Mon Apr 27 2020 - 11:50:30 PDT)
1. A_smr_A.pdb (4061 bytes)
2. A_smr_A.wa.pdb (4570 bytes)
3. frcmod.smr (3036 bytes)
4. leap.log (38115 bytes)
5. LEAPY (313 bytes)
6. SMR_RESIDUE.pdb (4031 bytes)
7. smr.ac (4447 bytes)
8. smr.prepin (3048 bytes)
Re: [AMBER] minimizing a pyridine in water Debarati DasGupta (Mon Apr 27 2020 - 11:53:48 PDT)
1. 3C68E36E6DE845A08FD0476A3C40D58F.png (132501 bytes)
Re: [AMBER] wrong geometry amide nitrogen Arnaud Bondon (Wed Apr 29 2020 - 01:43:53 PDT)
1. data_testsirius4.rar (33082 bytes)
Re: [AMBER] nativecontacts Gustavo Seabra (Wed Apr 29 2020 - 05:56:19 PDT)
1. bonds.awk (2721 bytes)
Re: [AMBER] wrong geometry amide nitrogen Junmei Wang (Wed Apr 29 2020 - 07:12:46 PDT)
1. mytest.tar (419840 bytes)
Re: [AMBER] wrong geometry amide nitrogen Junmei Wang (Wed Apr 29 2020 - 07:36:21 PDT)
1. mytest.tar.gz (37897 bytes)
Re: [AMBER] wrong geometry amide nitrogen Arnaud Bondon (Thu Apr 30 2020 - 01:17:37 PDT)
1. bal2.pdb (9148 bytes)
2. cR9.pdb (25138 bytes)
3. PMB.pdb (26385 bytes)
4. tat2.pdb (24612 bytes)
5. PMB2.pdb (26215 bytes)

Amber Archive Apr 2020 by messages with attachments