DNA
polyA-polyT decamer tutorial
This page provides a summary containing links to all of the files referenced in the DNA PolyA-PolyT AMBER tutorial.
NO FILES
| polyAT_vac.prmtop, polyAT_vac.inpcrd polyAT_cio.prmtop, polyAT_cio.inpcrd polyAT_wat.prmtop, polyAT_wat.inpcrd |
polyAT_vac_init_min.in
polyAT_vac_init_min.out,
polyAT_vac_init_min.rst
polyAT_vac_md1_12Acut.in, polyAT_vac_md1_nocut.in
polyAT_vac_md1_12Acut.out,
polyAT_vac_md1_12Acut.rst,
polyAT_vac_md1_12Acut.mdcrd.gz
polyAT_vac_md1_nocut.out,
polyAT_vac_md1_nocut.rst,
polyAT_vac_md1_nocut.mdcrd.gz
polyAT_vac_md1_12Acut.summary.tar.gz, polyAT_vac_md1_nocut.summary.tar.gz
polyAT_vac_md1_12Acut.calc_rms,
polyAT_vac_md1_nocut.calc_rms
polyAT_vac_md1_12Acut.rms,
polyAT_vac_md1_nocut.rms
Trajectory 1 movie - in vacuo 12A cut off Small 7.4MB
Trajectory 2 movie - in vacuo no cut off: Side View: Small 1.1 MB, Large 2.7 MB Top View: Small 1.0 MB, Large 2.9 MB
polyAT_gb_init_min.out, polyAT_gb_init_min.rst
polyAT_gb_md1_12Acut.in, polyAT_gb_md1_nocut.in
polyAT_gb_md1_12Acut.out,
polyAT_gb_md1_12Acut.rst,
polyAT_gb_md1_12Acut.mdcrd.gz
polyAT_gb_md1_nocut.out,
polyAT_gb_md1_nocut.rst,
polyAT_gb_md1_nocut.mdcrd.gz
polyAT_gb_md1_12Acut.summary.tar.gz, polyAT_gb_md1_nocut.summary.tar.gz
polyAT_gb_md1_12Acut.calc_rms, polyAT_gb_md1_nocut.calc_rms
Trajectory 3 movie - Born Solvation Model 12A cut off (Small 5.4MB)
polyAT_wat_min1.out, polyAT_wat_min1.rst
polyAT_wat_min2.out, polyAT_wat_min2.rst
polyAT_wat.pdb, polyAT_wat_min2.pdb
polyAT_wat_md1.out, polyAT_wat_md1.rst, polyAT_wat_md1.mdcrd.gz
polyAT_wat_md2.out, polyAT_wat_md2.rst, polyAT_wat_md2.mdcrd.gz
polyAT_wat_md1+2.summary.tar.gz
polyAT_wat_calc_backbone_rms.in
Trajectory 4 movie - PolyA-PolyT Explicit TIP3P Water (small [13.6 MB])
polyAT_wat_reimage.ptraj
polyAT_wat_md_reimaged.mdcrd.gz
a-dna.nucgen.out, a-dna.nucgen.pdb
a-dna_charges_only.prmtop, a-dna_charges_only.inpcrd
a-dna_wat.prmtop, a-dna_wat.inpcrd
a-dna_min1.out, a-dna_min1.rst
a-dna_min2.out, a-dna_min2.rst
| Time Span (ps) | mdout | rstrt | mdcrd |
| 20 - 220 | a-dna_md2.out | a-dna_md2.rst | a-dna_md2.mdcrd.gz |
| 220 - 420 | a-dna_md3.out | a-dna_md3.rst | a-dna_md3.mdcrd.gz |
| 420 - 620 | a-dna_md4.out | a-dna_md4.rst | a-dna_md4.mdcrd.gz |
| 620 - 820 | a-dna_md5.out | a-dna_md5.rst | a-dna_md5.mdcrd.gz |
| 820 - 1020 | a-dna_md6.out | a-dna_md6.rst | a-dna_md6.mdcrd.gz |
| 1020 - 1220 | a-dna_md7.out | a-dna_md7.rst | a-dna_md7.mdcrd.gz |
| 1220 - 1420 | a-dna_md8.out | a-dna_md8.rst | a-dna_md8.mdcrd.gz |
| 1420 - 1620 | a-dna_md9.out | a-dna_md9.rst | a-dna_md9.mdcrd.gz |
| 1620 - 1820 | a-dna_md10.out | a-dna_md10.rst | a-dna_md10.mdcrd.gz |
combine_mdcrds_and_strip.ptraj
a-dna_0-1820ps.rmsfit,a-dna_0-1820ps_no_wat.mdcrd.gz