˵Ã÷£¬±¾ÊµÕ½½Ì³ÌÊÇAmberMDµÄ³õ²½tutorial£¬°³¸ù¾Ý¹ÙÍø£¬Ò»²½²½ÊµÕ½£¬È«²¿ÊǺÃʹµÄ£¬²Å¼Ç¼ÏÂÀ´£¬ÓëÖî¾ý¹²÷Ï¡£
http://ambermd.org/tutorials/basic/tutorial1/index.htm
Amberѧϰ£ºÄ£ÄâDNAµÄƬ¶Î £¨ÓÐЩ·Òë±í´ï£¬²»¾¡ÈçÈËÒ⣬¼ûÁ¡££©
Part 1 Introduction
¸ÃѧϰÊÖ²áÊ×ÏÈÑÝʾÁËÈçºÎ¹¹½¨Ò»¸öÊ®±¶Ìåpdb½á¹¹£¬²¢ÀûÓÃÕâ¸ö½á¹¹¹¹½¨sanderÔËÐбØÒªµÄÊäÈëÎļþ¡£MD·ÂÕæÄں˻ùÓÚAMBER14¡£
MD·ÂÕæÐèÒªÈô¸ÉÎļþ£¬Ö÷Òª°üÀ¨£º
prmtop ¨C ¸ÃÎļþ°üº¬·Ö×ÓµÄÍØÆ˽ṹ£¬ºÍ±ØÒªµÄÁ¦³¡²ÎÊý¡£
inpcrd (»òÒ»¸öÉÏ´ÎÔËÐвúÉúµÄ restrtÎļþx.rst) ¨C¸ÃÎļþ°üº¬Ô×Ó×ø±ê£¬»òÕßÒ²¿ÉÄÜ°üº¬ËٶȺÍÖÜÆÚÐԱ߽çºÐ×ӳߴçµÈÐÅÏ¢¡£periodic box dimensions.
mdin ¨C ¸ÃÎļþÊÇsanderµÄÊäÈëÎļþ(*.in)£¬°üº¬Ò»ÏµÁÐÎļþÃû¡¢ÓÃÓÚ¾ö¶¨·ÂÕæÀàÐͺͷÂÕæÑ¡ÏîµÄ¿ØÖƱäÁ¿¡£
¸Ã½Ì³ÌµÚÒ»²¿·ÖÊÇ£¬ÔÛÃÇÏÈÓÃAMBERTOOL´´½¨prmtopºÍinpcrdÎļþ£¬²¢·Ö±ðÖÃÓÚÕæ¿ÕϵͳºÍÈܼÁϵͳ¡£È»ºóÖ´ÐÐ×îС»¯¡¢MD·ÂÕ棬×îÖյõ½·ÂÕæºóµÄDNA¡£
ÓÉÓÚʹÓÃÏÔʽÈܼÁ½øÐÐÕâЩģÄâ¿ÉÄܺܰº¹ó£¬ÎÒÃÇ»¹½«Ê¹ÓÃһЩģÐÍ£¬ÆäÖÐÒþº¬µØ°üº¬ÈܼÁЧӦ¡£
Part 2 ´´½¨Ë«Á´DNA polyA-polyT
1.ÓÃNAB´´½¨DNAË«ÂÝÐý²¢²úÉú¿ÉÓõÄÎļþ
(1)´´½¨Ò»¸öÎļþnuc.nab,дÈ룺
molecule m;
m = fd_helix( "abdna", "aaaaaaaaaa", "dna" );
putpdb( "nuc.pdb", m, "-wwpdb"
(2)ÔËÐÐÕâ¸öÎļþ£º
nab nuc.nab
./a.out
Ö®ºó½«²úÉúÒ»¸önuc.pdbÎļþ£¬Õâ¸öÎļþÊÇË«ÂÝÐý½á¹¹Ä£ÐÍ¡£ &--Èç¹ûÒѾÓÐpdbÎļþ£¬Ö±½Ó´ÓµÚÈý²½¿ªÊ¼ --songjun
(3)½«Õâ¸öÎļþµ¼ÈëleapÖУº
ÔÚÖÕ¶ËÊäÈëtleap,
ÔÙÊäÈëÁ¦³¡ source leaprc.ff99SB,
ÔÚ¹ÙÍø http://ambermd.org/tutorials/basic/tutorial1/section2.htm
ÖÐÓйØÓÚÁ¦³¡µÄ˵Ã÷£¬ÔÚÔçÆÚ°æ±¾(amber10 or 11)ÖÐÍƼöÓÃff99SB£¬µ«ÔÚamber12ÖÐÍƼöÓÃff12SB£¬ÔÚamber14ÖÐÍƼöff14SB£¨ËüÊÇff99SBµÄÓÅ»¯°æ£©
¿´amber°æ±¾Ó㺠echo $AMBERHOME
source leaprc.ff14SB
µ¼ÈëpdbÎļþ£º> dna1= loadpdb "nuc.pdb"
ÔÚtleap´°¿ÚÖÐÊä³ö£ºLoading PDB file: ./nuc.pdb total atoms in file: 638 ˵Ã÷µ¼ÈëÕýÈ·¡£
(4)²úÉú.prmtopºÍ.inpcrdÎļþ£º
±£´æ£º> saveamberparm dna1 polyAT_vac.prmtop polyAT_vac.inpcrd
»áÊä³ö£º
Checking Unit.
WARNING: The unperturbed charge of the unit: -18.000000 is not zero.
-- ignoring the warning.
Building topology.
Ëü½«´´½¨Á½¸öÎļþ:
polyAT_vac.prmtop£ºÁ¦³¡²ÎÊý/ÍØÆËÎļþ¡£ËüÊǾ²Ì¬µÄ£¬ÔÚÄ£ÄâµÄ¹ý³ÌÖв»»á·¢Éú±ä»¯¡£
polyAT_vac.inpcrd£º×ø±ê£¬²»ÊǾ²Ì¬µÄÔÚÄ£ÄâÖлᷢÉú±ä»¯¡£
(5)¼ÓÖÐÐÔ»¯Àë×Ó£º
> addions dna1 Na+ 0 (0Òâζ×ÅÖÐÐÔ»¯)
½«Êä³ö
addions dna1 Na+ 0
18 Na+ ions required to neutralize.
Adding 18 counter ions to "dna1" using 1A grid
Grid extends from solute vdw + 3.65 to 9.75
Resolution: 1.00 Angstrom.
grid build: 0 sec
(no solvent present)
Calculating grid charges
charges: 1 sec
Placed Na+ in dna1 at (6.44, 3.95, 17.79).
Placed Na+ in dna1 at (5.44, -5.05, 10.79).
Placed Na+ in dna1 at (-10.56, 5.95, 13.79).
Placed Na+ in dna1 at (-10.56, -6.05, 19.79).
Placed Na+ in dna1 at (-1.56, 11.95, 9.79).
Placed Na+ in dna1 at (-10.56, -4.05, 6.79).
Done adding ions.
²úÉúÖÐÐÔ»¯µÄprmtopºÍinpcrdÎļþ£º
> saveamberparm dna1 polyAT_cio.prmtop polyAT_cio.inpcrd
Êä³ö£ºpolyAT_cio.prmtop, polyAT_cio.inpcrd
×îÖÕµÄÄ¿µÄÊǽ¨Á¢´øÓп¹ÐÔÀë×ӵĿÉÈܵÄDNAÎļþ£¬¿¹ÐÔÒѽ¨Á¢£¬½ÓÏÂÀ´´´½¨¿ÉÈÜÐÔµÄÎļþ£¬Ò²¾ÍÊǼÓË®¡£
> dna2 = copy dna1
> solvatebox dna1 TIP3PBOX 10.0
solvatebox dna1 TIP3PBOX 12.0 ¾ØÐκÐ×Ó£¬³ß´ç12A
½«Êä³ö
> solvatebox dna1 TIP3PBOX 8.0
Solute vdw bounding box: 27.738 26.738 40.099
Total bounding box for atom centers: 43.738 42.738 56.099
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: 46.743 45.963 58.910 angstroms.
Volume: 126564.801 A^3
Total mass 56296.124 amu, Density 0.739 g/cc
Added 2767 residues.
> solvateoct dna2 TIP3PBOX 10.0 °ËÃæÌåºÐ×Ó£¬³ß´ç10A
solvatebox dna2 TIP3PBOX 12.0
saveamberparm dna2 polyAT_wat.prmtop polyAT_wat.inpcrd
Output files: polyAT_wat.prmtop, polyAT_wat.inpcrd
savepdb DNA1 XXX.pdb &±£´æpdbµÄÃüÁî
µ½ÏÖÔÚÒѾ²úÉúÔËÐÐ×îС»¯ºÍ·Ö×Ó¶¯Á¦Ñ§µÄÎļþ¡£Ï²¿·Ö½«ÒªÓõ½¡£
&--------- ÖÁ´ËÐèÒªÍ˳ötleap, ÓÃÃüÁîquit £¡ ----------&
Part 3 ×îС»¯ºÍ·Ö×Ó¶¯Á¦Ñ§ÔËÐÐ
(1)×îС»¯ Ä¿µÄ£ºÎªÁËÈ¥³ý»µµÄÁªÏµ
sanderµÄÓï·¨£ºsander [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt[-ref refc] [-x mdcrd] [-v mdvel] [-e mden] [-inf mdinfo]
[]ÖÐÊÇ¿ÉÑ¡Ïî
¿ÉÑ¡ÏîΪָ¶¨Ê±£¬ÏµÍ³Ä¬ÈϲÉÓÃĬÈÏÖµ¡£
-O ¸²¸ÇÔÓеÄÊä³öÎļþ£»
-i ÊäÈëÎļþµÄÃû×Ö, ĬÈÏÊÇmdinÎļþ(*.in)£»
-o Êä³öÎļþÃû,ĬÈÏ mdout (*.out)£»
-p ²ÎÊý/ÍØÆËÎļþ,ĬÈÏ prmtop£»
-c ×ø±êÎļþ,ĬÈÏ inpcrd£»
-r ±¾´ÎMD»ò×îС»¯µÄ×ø±êÉèÖÃÎļþ£¬Ä¬ÈÏrestrt (*.rst)£»
-ref λÖÃÔ¼ÊøµÄ×ø±ê²Î¿¼Îļþ, ÊÇ¿ÉÑ¡Ïî,ĬÈÏ refc (*.rst»òinpcrd)£»
-x MDµÄ¹ì¼£Îļþ (Õë¶ÔMD·ÂÕ棬ÈôÊÇ×îС»¯£¬ÎÞ´ËÏî)£¬Ä¬ÈÏmdcrd£»
-v MDµÄËÙ¶ÈÎļþ£¬¿ÉÑ¡Ïî(if running MD)£¬Ä¬ÈÏmdvel £»
-e MDµÄÄÜÁ¿×ܽáÎļþ£¬¿ÉÑ¡Ïî (if running MD)£¬Ä¬ÈÏ mden.
-inf ×îС»¯Ê±Ã¿´ÎдÈëÄÜÁ¿ÐÅÏ¢µÄ×ܽáÎļþ£¬ÔÚcheck·ÂÕæ¹ý³ÌʱºÜÓÐÓã¬Ä¬ÈÏ mdinfoÎļþ¡£
ÄÜÁ¿ÓÅ»¯ÓÉsanderÄ£¿éÍê³É£¬ÔËÐÐsanderÖÁÉÙÐèÒªÈý¸öÊäÈëÎļþ£¬·Ö±ðÊÇ·Ö×ÓµÄÍØÆËÎļþ£¬×ø±êÎļþÒÔ¼°sanderµÄ¿ØÖÆÎļþ¡£ÏÖÔÚ·Ö×ÓµÄÍØÆËÎļþºÍ×ø±êÎļþÒѾÍê³É£¬ÐèÒª½¨Á¢mdinÊäÈëÎļþ :
polyAT_vac_init_min.inÖÐдÈ룺
polyA-polyT 10-mer: initial minimisation prior to MD
&cntrl
imin = 1,
maxcyc = 500,
ncyc = 250,
ntb = 0,
igb = 0,
cut = 12
/
½ÓÏÂÀ´ÔÛÃǵÚÒ»´Î²ÉÓà sanderÃüÁîÀ´ÔËÐÐ for the first time
ÓÃsanderÔËÐÐ×îС»¯£º
ÔÚ¹¤×÷Ŀ¼ÏÂÖÕ¶ËÊäÈ룺
sander -O -i polyAT_vac_init_min.in -o polyAT_vac_init_min.out -c polyAT_vac.inpcrd -p polyAT_vac.prmtop -r polyAT_vac_init_min.rst
Input files: polyAT_vac_init_min.in, polyAT_vac.inpcrd, polyAT_vac.prmtop
Output files: polyAT_vac_init_min.out, polyAT_vac_init_min.rst
ÕâÒ»²½ÔËÐбȽϿ죬´óÔ¼ÐèÒª¼¸ÃëµÄʱ¼ä¡£
ÕâÒ»²½Éú²úµÄ.rstÎļþÊÇ×ø±êÎļþ£¬ºÜ¹Ø¼ü¡£
´ËÍ⣬´ò¿ªpolyAT_vac_init_min.outÄܹ»·¢ÏÖÄÜÁ¿ÔÚµÚÒ»²½ºÍ×îºóÒ»²½µÄ±ä»¯£º
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.4123E+03 1.9444E+01 9.4276E+01 C2' 634
NSTEP ENERGY RMS GMAX NAME NUMBER
500 -2.3331E+03 6.1397E-01 3.8981E+00 C6 208
ÀûÓÃ×ø±êÎļþ(.rst)´´½¨ PDBÎļþ
> ambpdb -p polyAT_vac.prmtop < polyAT_vac_init_min.rst > polyAT_vac_init_min.pdb
Éú³ÉеÄpdbÎļþpolyAT_vac_init_min.pdb
Õæ¿ÕÖÐÔËÐÐ MD
ÎÒÃǽ«ÔËÐÐÀ´Á½¸ö£ºÒ»¸ö½Ø¶ÏֵΪ12°££¬Ò»¸öΪ0
´´½¨polyAT_vac_md1_12Acut.inÎļþ£¬Ð´È룺
10-mer DNA MD in-vacuo, 12 angstrom cut off
&cntrl
imin = 0, ntb = 0, //imin = 0,¹Ø±Õ×îС»¯ £»ntb = 0,ûÓÐÖÜÆÚÐԱ߽çÌõ¼þ(ûºÐ×ÓË®)
igb = 0, ntpr = 100,
ntwx = 100, //igb = 0,ûÓÐÈܼÁ´æÔÚ£»ºóÃæµÄÿһ°Ù²½Êä³öÒ»¸ö¹ì¼£×ø±ê
ntt = 3, gamma_ln = 1.0, // ntt = 3,ºãÎÂÆ÷(Langevin dynamics);
tempi = 300.0, temp0 = 300.0, //ζÈΪ300K
nstlim = 100000, dt = 0.001, //ÔËÐÐ100000²½£¬Ã¿²½Îª0.001Ãë
cut = 12.0 //½Ø¶ÏֵΪ12°£
/
¿ÕÁ½ÐÐ
´´½¨polyAT_vac_md1_nocut.inÎļþ£¬Ð´È룺
10-mer DNA MD in-vacuo, no cut off
&cntrl
imin = 0, ntb = 0,
igb = 0, ntpr = 100, ntwx = 100,
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0,
nstlim = 100000, dt = 0.001,
cut = 999
/
½ÓÏÂÀ´£¬ÔÙ´ÎÔËÐÐsanderÃüÁ
µÚÒ»¸ö£º
> sander -O -i polyAT_vac_md1_12Acut.in -o polyAT_vac_md1_12Acut.out -c polyAT_vac_init_min.rst -p polyAT_vac.prmtop -r polyAT_vac_md1_12Acut.rst -x polyAT_vac_md1_12Acut.mdcrd
Õâ¸öÃüÁîÖÁÉÙÐèÒª10·ÖÖÓ×óÓÒ¡£
µÚ¶þ¸ö£º
> sander -O -i polyAT_vac_md1_nocut.in -o polyAT_vac_md1_nocut.out -c polyAT_vac_init_min.rst -p polyAT_vac.prmtop -r polyAT_vac_md1_nocut.rst -x polyAT_vac_md1_nocut.mdcrd
Õâ¸öÒ²ÐèÒª10·ÖÖÓ×óÓÒ¡£
¿ÉÓÃtopÃüÁî¿´sanderÊÇ·ñÔËÐÐÍê±Ï¡££¨ÉÏÊöÃüÁî½áβҲ¿É¼Ó·ûºÅ & £©
¿´ÔËÐеĽø³Ì£ºÊäÈ룺tail -f polyAT_vac_md1_12Acut.out
ÊäÈëÎļþ°üÀ¨: polyAT_vac_md1_12Acut.in, polyAT_vac_md1_nocut.in, polyAT_vac_init_min.rst, polyAT_vac.prmtop
Êä³öÎļþ°üÀ¨: polyAT_vac_md1_12Acut.out, polyAT_vac_md1_nocut.out, polyAT_vac_md1_12Acut.rst, polyAT_vac_md1_nocut.rst, polyAT_vac_md1_12Acut.mdcrd, polyAT_vac_md1_nocut.mdcrd
½á¹û·ÖÎö
(1) ´ÓmdoutÎļþÖÐÌáÈ¡ÄÜÁ¿£º½Ø¶ÏÖµ12°£µÄÎļþ:
mkdir polyAT_vac_md1_12Acut
cd polyAT_vac_md1_12Acut
>process_mdout.perl ../polyAT_vac_md1_12Acut.out
ͬÑù´¦ÀínocutµÄÎļþ
mkdir polyAT_vac_md1_nocut
cd polyAT_vac_md1_nocut
>process_mdout.perl ../polyAT_vac_md1_nocut.out
(2)½ÓÏÂÀ´£¬»¹ì¼££º
xmgrace ./polyAT_vac_md1_12Acut/summary.EPTOT ./polyAT_vac_md1_nocut/summary.EPTOT
xmgraceÃüÁîÓÐÎÊÌ⣬ÊÇÒòΪûÓа²×°Ïà¹Øxmgrace×é¼þ¡£Ëüʵ¼ÊÉÏÊÇÒ»¿î»ÇúÏßµÄÈí¼þ£¬ÔÛÃÇ¿ÉÒÔcopy³öÁ½¸ösummary.EPTOTÎļþ£¬ÓÃmatlabÀ´»ÇúÏߣ¬Ò²ÊÇÒ»Ñù¡£
×¢£ºsummary.EPTOTÖеÄÊý¾Ýժ¼ÈçÏ£º
0.000 -2267.9419
0.100 -1570.4415
0.200 -1424.1312
0.300 -1513.0011
0.400 -1247.5700
0.500 -1101.3187
0.600 -1003.6084
0.700 -1183.8510
0.800 -1137.9767
0.900 -915.5758
1.000 -656.8817
1.100 -933.2193
1.200 -990.0922
1.300 -885.8356
1.400 -916.7535
ÎÊÌâ½â¾ö£¬½Ó×ÅÍùÏÂ×ß¡£
(3)¼ÆËãRmsdÖµËæʱ¼äµÄ±ä»¯£º
Ê×ÏȽ¨Á½¸öÎļþ£ºpolyAT_vac_md1_12Acut.calc_rms ºÍ polyAT_vac_md1_nocut.calc_rms
·Ö±ðдÈ룺
trajin polyAT_vac_md1_12Acut.mdcrd
rms first mass out polyAT_vac_md1_12Acut.rms time 0.1
trajin polyAT_vac_md1_nocut.mdcrd
rms first mass out polyAT_vac_md1_nocut.rms time 0.1
ÔËÐÐ cpptraj ÃüÁÈçÏÂ:
$AMBERHOME/bin/cpptraj -p polyAT_vac.prmtop -i polyAT_vac_md1_12Acut.calc_rms
$AMBERHOME/bin/cpptraj -p polyAT_vac.prmtop -i polyAT_vac_md1_nocut.calc_rms
ÔËÐнá¹û´óÖÂÈçÏ£º
CPPTRAJ: Trajectory Analysis. V15.00
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
Reading 'polyAT_vac.prmtop' as Amber Topology
INPUT: Reading Input from file polyAT_vac_md1_12Acut.calc_rms
[trajin polyAT_vac_md1_12Acut.mdcrd]
Reading 'polyAT_vac_md1_12Acut.mdcrd' as Amber Trajectory
[rms first mass out polyAT_vac_md1_12Acut.rms time 0.1]
RMSD: (*), reference is first frame (*), with fitting, mass-weighted.
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES:
0: 'polyAT_vac.prmtop', 638 atoms, 20 res, box: None, 2 mol, 1000 frames
INPUT TRAJECTORIES:
0: 'polyAT_vac_md1_12Acut.mdcrd' is an AMBER trajectory, Parm polyAT_vac.prmtop (reading 1000 of 1000)
Coordinate processing will occur on 1000 frames.
TIME: Run Initialization took 0.0001 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'polyAT_vac.prmtop' (1 actions):
0: [rms first mass out polyAT_vac_md1_12Acut.rms time 0.1]
Target mask: (638)
Reference mask: (638)
----- polyAT_vac_md1_12Acut.mdcrd (1-1000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 1000 frames and processed 1000 frames.
TIME: Trajectory processing: 0.1576 s
TIME: Avg. throughput= 6345.0166 frames / second.
ACTION OUTPUT:
DATASETS:
1 data set:
RMSD_00000 "RMSD_00000" (double, rms), size is 1000
DATAFILES:
polyAT_vac_md1_12Acut.rms (Standard Data File): RMSD_00000
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.1940 seconds.
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
Theory Comput., 2013, 9 (7), pp 3084-3095.
»á²úÉúÁ½¸öÎļþ£ºpolyAT_vac_md1_12Acut.rms £¬polyAT_vac_md1_nocut.rms
È»ºó¿ÉÒÔ»æÖÆrmsdËæʱ¼ä±ä»¯ÇúÏßÁË£º
>xmgrace polyAT_vac_md1_12Acut.rms polyAT_vac_md1_nocut.rms
ͬÑù¿ÉÒÔÓÃmatlabÀ´»¡£ ¹Ù·½ÍøÕ¾µÄTutorialÊǸöºÃ¶«Î÷£¬´íÎó±È½ÏÉÙ£¬ºÜȨÍþ¡£
VMDʹÓ÷½·¨-windows
ÓÃVMD¿ÉÊÓ»¯¹Û²âsimualtion¹ì¼£
http://ambermd.org/tutorials/basic/tutorial1/section3.htm
(1)ÏÂÔØVMDÈí¼þwindows°æ±¾µ½×Ô¼ºµÄµçÄÔ¡£
https://www.ks.uiuc.edu/Research/vmd/
ÕâÊÇÒÁÀûŵÒÁ´óѧÏãéÄ·ÖУµÄ²úÆ·¡£
(2)°²×°VMD,²¢Æô¶¯ File -> New Molecule
Ê×ÏÈ×°ÔØpolyAT_vac.prmtop Îļþ£¬
È»ºóÔÙ×°Ôع켣Îļþ polyAT_vac_md1_12Acut.mdcrd £¬¸ÃÎļþÒ»°ã½Ï´ó¡£
×°ÔØokºó£¬¿ÉÒÔ¿´µ½ÈçÏ¿ÉÊÓ»¯½çÃ棺
£¨ÂÛ̳ÖÐÈçºÎ²åÈëͼƬ£¬°³»¹Ã»Ñ§»á£¬ËùÒÔÕâÀïµÄͼ¾Í²»ÏÔʾÁË ¡££©
Part 4 ÒþʽÈܼÁÖÐ×îС»¯²¢ÔËÐÐMD
ÉÏÊöSectionÒ»Ö±ÔÚÕæ¿ÕÖÐ(Vacuo)Ä£ÄâMD£¬½ÓÏÂÀ´ÔÚÒþʽÈܼÁ(implicit solvent)ÖÐÔËÐÐMD
(1) ÔÚMDÄ£ÄâÇ°£¬ÊÍ·ÅϵͳRelaxing the System Prior to MD
ÕâÒ»²½£¬»¹Ê¹ÓÃÔÀ´µÄprmtop and inpcrd Îļþ£¬(polyAT_vac.prmtop, polyAT_vac.inpcrd)
Ê×ÏÈ´´½¨ÊäÈëÎļþ(polyAT_gb_init_min.in):
polyA-polyT 10-mer: initial minimization prior to MD GB model
&cntrl
imin = 1,
maxcyc = 500,
ncyc = 250,
ntb = 0,
igb = 1,
cut = 12
/
¿ÕÐÐ
ÔËÐÐsander ÃüÁ×îС»¯
$AMBERHOME/bin/sander -O -i polyAT_gb_init_min.in -o polyAT_gb_init_min.out -c polyAT_vac.inpcrd -p polyAT_vac.prmtop -r polyAT_gb_init_min.rst
ÊäÈë/Êä³öÎļþÊÇ£º
Input files: polyAT_gb_init_min.in, polyAT_vac.inpcrd, polyAT_vac.prmtop
Output files: polyAT_gb_init_min.out, polyAT_gb_init_min.rst
ÕâÒ»²½´óÔ¼ÐèÒª30Ãë¡£
´ò¿ª(polyAT_gb_init_min.out)Îļþ¿ÉÒÔ·¢ÏÖ£¬ÄÜÁ¿ÊÕÁ²
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -2.2247E+03 1.9139E+01 9.3100E+01 C2' 634
NSTEP ENERGY RMS GMAX NAME NUMBER
500 -3.3168E+03 8.7962E-01 6.8734E+00 N1 618
Éú³ÉеÄPDBÎļþ£º
Again we can create PDB files for the start (polyAT_vac.inpcrd) and final structures (polyAT_gb_init_min.rst). [polyAT_gb_init_min.pdb].
$AMBERHOME/bin/ambpdb -p polyAT_vac.prmtop -c polyAT_gb_init_min.rst > polyAT_gb_init_min.pdb
Ôʼ½á¹¹(green),ºÍ×îС»¯Ö®ºóµÄ(blue)
savepdb DNA1 XXX.pdb &±£´æpdbµÄÃüÁî
£¨2£©ÔÚ¹éÒ»»¯µÄ Born solvationÈܼÁÖÐÔËÐÐMD simulation
ÉÏÒ»½Ú£¬ÎÒÃÇÔÚÕæ¿ÕÖÐÔËÐÐvacuo£¬½á¹û²»ÄÜÁîÈËÂúÒ⣬ÄÇÊÇÒòΪËü²»ÊÇÕæʵµÄÉúÎïÌå»·¾³¡£ÕâÒ»½Ú£¬ÎÒÃÇÔÚBorn solvationÈܼÁÔÙ´ÎÔËÐÐMD¡£
Ê×ÏÈ£¬ÐèÒªÁ½¸öÀàËƵÄÊäÈëÎļþmdin
polyAT_gb_md1_12Acut.in :12.0 A long range cutoff, Generalized Born
polyAT_gb_md1_nocut.in : no long range cutoff, Generalized Born
polyAT_gb_md1_12Acut.in
10-mer DNA MD Generalise Born, 12A cut off
&cntrl
imin = 0, ntb = 0,
igb = 1, ntpr = 100, ntwx = 100,
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0,
nstlim = 100000, dt = 0.001,
cut = 12
/
¿Õ¸ñ
polyAT_gb_md1_nocut.in
10-mer DNA MD Generalise Born, no cut off
&cntrl
imin = 0, ntb = 0,
igb = 1, ntpr = 100, ntwx = 100,
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0,
nstlim = 100000, dt = 0.001,
cut = 999
/
½ÓÏÂÀ´µÄ·ÂÕ棬ÐèÒªÓõ½ÉÏÃæÉú²úµÄ×îС»¯½á¹¹Îļþ£º polyAT_gb_init_min.rst
MD·ÂÕæÃüÁîÈçÏ£º
$AMBERHOME/bin/sander -O -i polyAT_gb_md1_12Acut.in -o polyAT_gb_md1_12Acut.out -c polyAT_gb_init_min.rst -p polyAT_vac.prmtop -r polyAT_gb_md1_12Acut.rst -x polyAT_gb_md1_12Acut.mdcrd
$AMBERHOME/bin/sander -O -i polyAT_gb_md1_nocut.in -o polyAT_gb_md1_nocut.out -c polyAT_gb_init_min.rst -p polyAT_vac.prmtop -r polyAT_gb_md1_nocut.rst -x polyAT_gb_md1_nocut.mdcrd
Õâ¸öMDÔËÐÐʱ¼ä±È½Ï³¤£¬Ã¿¸ö¶¼ÐèÒª1-5¸ö¶àСʱ¡£
ÊäÈëÎļþÊÇ: polyAT_gb_md1_12Acut.in, polyAT_gb_md1_nocut.in, polyAT_gb_init_min.rst, polyAT_vac.prmtop
Êä³öÎļþ: polyAT_gb_md1_12Acut.out, polyAT_gb_md1_nocut.out, polyAT_gb_md1_12Acut.rst, polyAT_gb_md1_nocut.rst, polyAT_gb_md1_12Acut.mdcrd, polyAT_gb_md1_nocut.mdcrd
×¢£ºmdcrdÎļþ´óÔ¼15MB´óС¡£
ºÃ²»ÈÝÒ×£¬ÔËÐÐMD½áÊø£¬¿ÉÒÔ½øÐнá¹û·ÖÎöÁË¡£
£¨3£©½á¹û·ÖÎö
ÓÉÓÚÓÃÓÚ½á¹û·ÖÎöµÄÎļþ½Ï¶à£¬ÐèÒª´´½¨Á½¸öÎļþ¼Ð¡£
mkdir polyAT_gb_md1_12Acut
mkdir polyAT_gb_md1_nocut
cd polyAT_gb_md1_12Acut
process_mdout.perl ../polyAT_gb_md1_12Acut.out
cd ../polyAT_gb_md1_nocut
process_mdout.perl ../polyAT_gb_md1_nocut.out
cd ..
xmgrace ./polyAT_gb_md1_12Acut/summary.EPTOT ./polyAT_gb_md1_nocut/summary.EPTOT
×¢Ò⣺
xmgrace ./polyAT_gb_md1_12Acut/summary.EPTOT ./polyAT_gb_md1_nocut/summary.EPTOT
Õâ¸öÃüÁîÊÇÓÃÀ´»ÊÆÄÜÇúÏߵģ¬Ôںܶà·þÎñÆ÷ÉÏûÓа²×°Õâ¸ö×é¼þ¡£
Òò´Ë£¬ÎÒÃÇ¿ÉÒÔÓÃMatlab»òexcelÀ´¸ù¾Ýsummary.EPTOTµÄÊý¾Ý½øÐлæÖÆÇúÏߣ¬ÐÔÖÊÊÇÒ»ÑùµÄ¡£ÊÆÄÜÇúÏß´óÖÂÈçÏ£º
ÔÚ½ÓÏÂÀ´£¬ÎÒÃÇ·ÖÎö¾ù·½¸ùÎó²îRMSd
Ê×ÏÈ´´½¨cpptraj ÊäÈëÎļþ
polyAT_gb_md1_12Acut.calc_rmsÎļþ£º
trajin polyAT_gb_md1_12Acut.mdcrd
rms first mass out polyAT_gb_md1_12Acut.rms time 0.1
polyAT_gb_md1_nocut.calc_rmsÎļþ£º
trajin polyAT_gb_md1_nocut.mdcrd
rms first mass out polyAT_gb_md1_nocut.rms time 0.1
ÔËÐÐcpptrajÃüÁ
$AMBERHOME/bin/cpptraj -p polyAT_vac.prmtop -i polyAT_gb_md1_12Acut.calc_rms
$AMBERHOME/bin/cpptraj -p polyAT_vac.prmtop -i polyAT_gb_md1_nocut.calc_rms
µÃµ½Á½¸öÊä³öÎļþ£¬Îª¾ù·½²îÎļþ£º
polyAT_gb_md1_12Acut.rms
polyAT_gb_md1_nocut.rms
ͬÑù¿ÉÒÔÓÃMatlab»òexcel»æÖƾù·½²îÇúÏߣ¬´óÖÂÈçÏÂ
¸½£º×îºóÎÒÃÇ¿ÉÒÔÔÚ×Ô¼ºµÄµçÄÔÉÏÔËÐÐVMD£¬¿´DNA·ÂÕæÔËÐй켣¡£
Ê×ÏÈ×°ÔØÎļþpolyAT_vac.prmtop ²¢ then select AMBER7 Parm.
Loadºó£¬ÔÙ¼ÓÔØ12AµÄ¹ì¼£ÎļþpolyAT_gb_md1_12Acut.mdcrd
È»ºó¼´¿É²¥·Åvideo½øÐй켣¹Û²âÁË¡£ÈçÏÂͼ£º
Part 5 ÏÔʽÈܼÁÖÐ×îС»¯²¢ÔËÐÐMD (explicit solvent)
5.1)ƽºâ²¢·ÂÕæÈܼÁ»¯µÄ10±¶ÌåpolyAT
¶ÔÔÓÐÕæ¿ÕÖнṹ½øÐÐƽºâµÄÔÒò£¬¼°ÖÜÆÚÐԱ߽çÌõ¼þ¼ò½é
(1)³õ²½×îС»¯
·ÂÕæµÚÒ»²½£¬½¨Á¢ÊäÈëÎļþmdin
polyAT_wat_min1.in
polyA-polyT 10-mer: initial minimisation solvent + ions
&cntrl
imin = 1,
maxcyc = 4000,
ncyc = 2000,
ntb = 1,
ntr = 1,
cut = 10.0
/
Hold the DNA fixed
500.0
RES 1 20
END
END
Èç¹ûÊÇ60bp£¬Ôò¸ÄΪRES 1 120£¬Ô¼ÊøÔ×ÓÊÇ1µ½120£¨60¶Ô£©
·ÂÕæµÚ¶þ²½£¬sanderÃüÁîÔËÐÐ×îС»¯
£¨×¢Ò⣬ÎÒÃÇÔÚÃüÁîÐУ¨-ref£©ÉÏÓÐÒ»¸ö¶îÍâµÄÑ¡ÏÕâÆäʵÊÇÖ¸¶¨ÁËÐèÒªÔ¼ÊøµÄÔ×ӽṹ£¬ÔÚÕâÖÖÇé¿öÏ£¬ÎÒÃÇʹÓõÄÊÇinpcrdÎļþÖеijõʼ½á¹¹¡£ÎÒÃǽ«Ê¹ÓÃÔÚ±¾½Ì³Ì¿ªÊ¼Ê±´´½¨µÄÈܼÁ»¯prmtopºÍinpcrdÎļþ¡££©
$AMBERHOME/bin/sander -O -i polyAT_wat_min1.in -o polyAT_wat_min1.out -p polyAT_wat.prmtop -c polyAT_wat.inpcrd -r polyAT_wat_min1.rst -ref polyAT_wat.inpcrd
ÊäÈëÎļþÊÇ: polyAT_wat_min1.in, polyAT_wat.prmtop, polyAT_wat.inpcrd
Êä³öÎļþÊÇ: polyAT_wat_min1.out, polyAT_wat_min1.rst
Õâ¸ö×îС»¯¹ý³Ì´óÔ¼ÐèÒª3·ÖÖÓ¡£
Èç¹ûÔÚÕâÒ»²½½áÊøºó£¬ÎÒÃDz鿴.outÎļþ£¬¿ÉÒÔ·¢ÏÖ£¬van der Waals (VDWAALS and 1-4 VDW)ºÜ´ó£¬¾²µçÄÜelectrostatic energy (EEL)ϽµºÜ¶à£¬ËµÃ÷£¬Ë®ºÍDNAÓв»Á¼½Ó´¥£¬ÓÅ»¯Ò²ÐèÒª½øÒ»²½½øÐС£
(2)Õû¸öϵͳ×îС»¯
Ê×ÏÈÐèÒªÊäÈëÎļþmdin
polyAT_wat_min2.in
polyA-polyT 10-mer: initial minimisation whole system
&cntrl
imin = 1,
maxcyc = 4000,
ncyc = 2000,
ntb = 1,
ntr = 0,
cut = 10.0
/
È»ºó£¬ÓÃsanderÃüÁîÖ´ÐÐ×îС»¯£º
£¨×¢Ò⣬Õâ¸öÃüÁîʹÓÃÁËÉϸö²½ÖèµÄrestraintÎļþ.rst£¬Ëüº¬ÓÐÉÏ´Î×îС»¯ºóµÄ×îÖսṹ£¬Òò´Ë£¬²»ÐèÒª³õʼµÄinpcrd½á¹¹ÎļþÁË¡££©
$AMBERHOME/bin/sander -O -i polyAT_wat_min2.in -o polyAT_wat_min2.out -p polyAT_wat.prmtop -c polyAT_wat_min1.rst -r polyAT_wat_min2.rst
pmemd.cuda -O -i polyAT_wat_min2.in -o polyAT_wat_min2.out -p polyAT_wat.prmtop -c polyAT_wat_min1.rst -r polyAT_wat_min2.rst
ÊäÈëÎļþ: polyAT_wat_min2.in, polyAT_wat.prmtop, polyAT_wat_min1.rst (ÉÏÒ»²½µÄ½á¹¹Îļþ)
Êä³öÎļþ: polyAT_wat_min2.out, polyAT_wat_min2.rst
Õâ¸ö×îС»¯£¬´óÔ¼ÐèÒª6-20·ÖÖÓ¡£
ÕâÒ»²½×îС»¯ºó£¬ÎÒÃÇÐèÒª¿´¿´pdb½á¹¹ÒÀÈ»Îȶ¨£¬È»ºóÔÙ½øÐÐMD·ÂÕæ¡£
$AMBERHOME/bin/ambpdb -p polyAT_wat.prmtop < polyAT_wat.inpcrd > polyAT_wat.pdb
$AMBERHOME/bin/ambpdb -p polyAT_wat.prmtop < polyAT_wat_min2.rst > polyAT_wat_min2.pdb
Éú³ÉÁ½¸öpdbÎļþ£º(polyAT_wat.pdb, polyAT_wat_min2.pdb)£¬ÔÛÃÇ¿ÉÒÔÓÃVMD¹Û²ì¡£
ÔÚ±¾»úwindowsÉÏÆô¶¯VMD
vmd
File -> New Molecule (load the first pdb polyAT_wat.pdb)
(3) »ùÓÚÈܼÁ´ø¼ÓÈȺʹøÔ¼ÊøµÄMD·ÂÕæ
ÕâÊÇÒ»¸ö´øÈõλÖÃÔ¼ÊøµÄ20psµÄMD·ÂÕæ¡£
ÊäÈëÎļþpolyAT_wat_md1.in (ºóÃæÎÒÓиÄдµÄinÎļþ)
polyA-polyT 10-mer: 20ps MD with res on DNA
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 10000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000
/
Keep DNA fixed with weak restraints
10.0
RES 1 20
END
END
SanderÃüÁîÈçÏ£º
$AMBERHOME/bin/sander -O -i polyAT_wat_md1.in -o polyAT_wat_md1.out -p polyAT_wat.prmtop -c polyAT_wat_min2.rst -r polyAT_wat_md1.rst -x polyAT_wat_md1.mdcrd -ref polyAT_wat_min2.rst
pmemd.cuda -O -i polyAT_wat_md1.in -o polyAT_wat_md1.out -p polyAT_wat.prmtop -c polyAT_wat_min2.rst -r polyAT_wat_md1.rst -x polyAT_wat_md1.mdcrd -ref polyAT_wat_min2.rst
²ÉÓõÄÊÇÉϴεڶþ²½×îС»¯²úÉúµÄÔ¼ÊøÎļþxx_min2.rst
ÊäÈëÎļþ: polyAT_wat_md1.in, polyAT_wat.prmtop, polyAT_wat_min2.rst
Êä³öÎļþ: polyAT_wat_md1.out, polyAT_wat_md1.rst, polyAT_wat_md1.mdcrd
Õâ¸öMD¹ý³Ì´óÔ¼ÐèÒª30·ÖÖÓ¡£
(4) ¶ÔÕû¸öϵͳÔËÐÐƽºâ»¯µÄMD ·ÂÕæ
Ê×ÏÈ£¬ÊäÈëÎļþÉè¼ÆÔËÐÐʱ¼äÊÇ100ps£¬ÒÔ±ãÓгä×ãʱ¼ärelax¡£
polyAT_wat_md2.in
polyA-polyT 10-mer: 100ps MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 50000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000
/
ÕâÑù£¬ÉÏ´ÎÊÇ100Ö¡¹ì¼£Îļþ£¬Õâ´ÎÊÇ500Ö¡£¬¼ÓÆðÀ´ËùÒÔÊÇ600Ö¡¹ì¼£Îļþ(¼ûÏÂͼ)¡£
MDµÄsanderÃüÁîÈçÏ£º
$AMBERHOME/bin/sander -O -i polyAT_wat_md2.in -o polyAT_wat_md2.out -p polyAT_wat.prmtop -c polyAT_wat_md1.rst -r polyAT_wat_md2.rst -x polyAT_wat_md2.mdcrd
×¢£ºÕâ´ÎʹÓõÄrestrt ÎļþÊǸոÕMD·ÂÕ棨²»ÊÇ×îС»¯·ÂÕæÊä³öµÄrstÎļþ£©Êä³öµÄrstÎļþ£¬ÒòΪËüº¬ÓÐ×îÖÕµÄMD ¿ò¼Ü¡¢ËٶȺÍÈÜÒººÐ×ÓÐÅÏ¢¡£velocities and box information.
ÊäÈëÎļþ: polyAT_wat_md2.in, polyAT_wat.prmtop, polyAT_wat_md1.rst
Êä³öÎļþ: polyAT_wat_md2.out, polyAT_wat_md2.rst, polyAT_wat_md2.mdcrd
ÕâÀïµÄxx.mdcrdÎļþºÜ´ó£¬Ô¼45MB¡£ÔËÐÐʱ¼ä´óÔ¼2Сʱ¡£Èç¹ûÊÇ20¼î»ù¶Ô£¬ÔËÐг¬¹ý12Сʱ¡£
MDºǫ́ÔËÐз½·¨£º
nohup + ÃüÁî + &
ÔÙ°´ ctrl + d »òexit Í˳öshell¾Í¿ÉÒÔÁË¡£
5.2) ·ÖÎö½á¹ûÒÔÈ·¶¨Îȶ¨ÐÔ
ÕâÒ»²½ÓÐÐí¶à²ÎÊýÐèÒª·ÖÎö¼ø¶¨£¬ÒÔ±ãÈ·ÈÏƽºâµÄÖÊÁ¿¡£°üÀ¨£º
Potential, Kinetic and Total energy
Temperature
Pressure
Volume
Density
RMSd ÊÆÄÜ¡¢¶¯ÄÜ¡¢×ÜÄÜÁ¿
ζÈ
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Ìå»ý
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(1) ·ÖÎöÊä³öÎļþ
ÔÚamberÃüÁîÐÐÖÐн¨Îļþ¼Ð£º
mkdir analysis
cd analysis
process_mdout.perl ../polyAT_wat_md1.out ../polyAT_wat_md2.out
ÔÚanalysisÎļþÖн«Êä³öÐí¶àsummaryÎļþ£¬±ÈÈçsummary.EPTOT£¬summary.EKTOT£¬ summary.ETOTµÈ¡£
¿ÉÒÔÓÃmatlab »òexcel »³öÕâЩÎļþ(¶¼¿ÉÓÃultraedit´ò¿ª)ÖеÄÊý¾ÝÇúÏߣ¬ÈçÏÂͼËùʾ¡£
(2) ·ÖÎö¹ì¼£
·ÖÎöDNAµÄ¹Ç¼Ü£¬ÊäÈëÎļþÊÇ£º
polyAT_wat_calc_backbone_rms.in
trajin polyAT_wat_md1.mdcrd
trajin polyAT_wat_md2.mdcrd
rms first out polyAT_wat_backbone.rms @P,O3',O5',C3',C4',C5' time 0.2
¼ÆËã¹Ç¼ÜµÄRMSd£º
$AMBERHOME/bin/cpptraj -p polyAT_wat.prmtop -i polyAT_wat_calc_backbone_rms.in
Êä³öÎļþ£ºpolyAT_wat_backbone.rms
ͬÑù¿ÉÒÔÓÃmatlab»³örmsµÄ×ßÊÆͼ¡£
ÓÉÓÚÇ°20 psÊÇÓÐÔ¼ÊøµÄ£¬Òò´ËRMSdÎȶ¨£¬¶øºóÔÚÈ¥³ýÔ¼Êøºó£¬RMSdѸËÙ×߸ߡ£
(3) ¿ÉÊÓ»¯MD½á¹û
Óñ¾»úµÄVMDÈí¼þ
Step 1£º load the prmtop file (polyAT_wat.prmtop) £¬×¢ÒâҪѡÔñ£º "AMBER7 Parm"
Step 2£º load the two trajectory files (polyAT_wat_md1.mdcrd, polyAT_wat_md2.mdcrd), ×¢Ò⣺Õâ´ÎÑ¡ÏîÊÇ AMBER Coordinates with Periodic Box as file type since our simulations are now periodic boundary runs with the box information stored in the trajectory file.
0ps 120ps
¿ÉÒÔ·¢ÏÖ£¬ÔÚMDºó³Ì£¬ÒòΪȥ³ýÁËÔ¼Êø£¬Ë®ÅÜÁË¡£
Èç¹ûֻѡÖС°all not water¡±¿É·¢ÏÖ£¨·½·¨ÈçÇ°ÃæµÄVMD²Ù×÷ËùÊö£©£¬¹Ç¼ÜÒ²Êܵ½Íþв¡£
(4) °Ñ¹ì¼£ÖØÓ³Éäµ½³õʼºÐ×Ó
ÊäÈëÎļþÊÇ£º
polyAT_wat_reimage.ptraj £¨´ËÄËÎļþÃû£©
trajin polyAT_wat_md1.mdcrd
trajin polyAT_wat_md2.mdcrd
trajout polyAT_wat_md_reimaged.mdcrd
center :1-20
image familiar
ÓÃamberÃüÁ
$AMBERHOME/bin/cpptraj -p polyAT_wat.prmtop -i polyAT_wat_reimage.ptraj
Éú²úеĹ켣ÎļþpolyAT_wat_md_reimaged.mdcrd£¨±È½Ï´ó£¬ÖÁÉÙ100MB¶à£©
Õâ»á½«md2¹ì¼£Îļþ¸½¼Óµ½md1Îļþ£¬¸ü¸Ä¹ì¼££¬Ê¹²Ð²î1µ½20µÄ¼¸ºÎÖÐÐÄ·ÅÖÃÔÚԵ㣬Ȼºó½«³õʼºÐ×ÓÍⲿµÄËùÓÐ×ø±êÓ³Éäµ½ºÐ×ÓboxÄÚ²¿¡£ÊìϤµÄ¹Ø¼ü×ÖÈ·±£cpptraj½«ºÐ×Óд³ÉÊìϤµÄ½Ø¶Ï°ËÃæÌå¶ø²»ÊÇĬÈϵÄÈýб³ÉÏñ¡£×îºó£¬×ª»»ºóµÄ¹ì¼£½«±»Ð´ÈëpolyAT_wat_md_reimaged.mdcrd¡£
ÏÖÔÚ£¬ÔÛÃÇ¿ÉÒÔÔÚVMDÖдò¿ª´Ë¹ì¼£Îļþ£¬»á·¢ÏÖÎÒÃǵķÉË®µÎ¸üÍêÕû¡£ÔÚvmdÖнøÐбíʾ¡¢È¥³ýË®²¢½ö¹Û²ìDNAµÈ¡£¹Û²ìÔڹرÕÔ¼ÊøºóµÄÇ°20psºóDNA·Ö×ӵĶ¯Ì¬ÈçºÎ±ä»¯¡£´ËÍ⣬ÎÒÃÇ»¹¿ÉÒԹ۲쵽£¬ÏÖÔÚµÄDNAÁ´±ÈÔÚÕæ¿ÕÄ£ÄâÖиüÎȶ¨¡£
5.3) Summary
Õâ¸ö½Ì³ÌÖ÷Òª°üº¬Á˳õʼPDBÎļþµÄ´´½¨£¬ÒÔ¼°pdbÎļþÐÞ¸Ä(±ÈÈç¼ÓÈëÖÐÐÔÔ×Ó£¬¼ÓË®ºÐ×ÓµÈ)£¬ÒÔÊÊÓ¦LEaP¼ÓÔØ£¨tleapÓУ¬xleapûÓУ©¡£´ËÍ⣬»¹°üº¬ÈçºÎÖк͸ÃDNA½á¹¹£¬ÈçºÎÈܽâÔÚË®ÖУ¬ÈçºÎ´´½¨MDÊäÈëÎļþ(xx.in)£¬ÒÔ¼°ÈçºÎ²ÉÓÃsanderÃüÁîÔËÐÐMD¡£
ÐèҪעÒâµÄÊÇ£¬ÔÛÃǵÃѧ»áÊäÈëÎļþÖÐÿһÐвÎÊýµÄ¾ßÌ庬ÒåºÍÓ÷¨£¬È»ºóÊÇÔÚÕæ¿Õ¡¢ÒþÐÔÈܼÁ¡¢ÏÔÐÔÈܼÁÖÐÔËÐÐMD·ÂÕæ¡£ÔÚ¸ÃtutorialÖУ¬»¹ÓÐ×îС»¯¡¢Æ½ºâµÈ¸ÅÄîÐèÒªÕÆÎÕ¡£×îºó£¬¼òµ¥µÄ½á¹û·ÖÎöºÍ¹ì¼£Îļþ¿ÉÊÓ»¯Ò²ÊÇÔÛÃÇÐèÒªÁ˽âµÄ¡£ÓÈÆäÊÇVMDÈí¼þ¹¦ÄÜÇ¿´ó£¬²»½ö¿ÉÊÓ»¯£¬»¹¿ÉÒÔ½øÐÐÆ×ÃܶȼÆËãºÍ¾ßÓÐÐźŴ¦Àísignal processing¹¦ÄÜ¡£
×¢£º
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Georgecumt ÓÚ Library of Lancaster University, U.K. 2018.11.12. |