4
鍙楁帶鍒嗗瓙鍔ㄥ姏瀛︽ā鎷?/p>
(Steered Molecular Dynamics)
鎵�璋撳彈鎺у垎瀛愬姩鍔涘妯℃嫙锛?/p>
S
teered
M
olecular
D
ynamics
锛?/p>
SMD
锛?/p>
锛屽氨鏄寚鍦ㄨ繘琛?/p>
鍒嗗瓙鍔ㄥ姏瀛︽ā鎷熸椂锛?/p>
浜轰负鍦扮粰鍒嗗瓙涓殑鏌愪釜鎴栨煇鍑犱釜鍘熷瓙鏂藉姞涓�涓亣鎯崇殑澶栧姏锛?/p>
鎴栬�呬汉涓哄湴
鍥哄畾鏌愪釜鎴栨煇鍑犱釜鍘熷瓙鐨勪綅缃�?/p>
浠庤�屾帶鍒舵暣涓垎瀛愮殑琛屼负銆?/p>
鎴戜滑鍓嶉潰杩涜鐨勫姩鍔涘妯℃嫙閮芥槸
閫氳繃鍚勭鍙傛暟璁剧疆锛?/p>
灏介噺閫艰繎铔嬬櫧璐ㄥ垎瀛愬湪婧舵恫浣撶郴涓殑鐪熷疄鐘舵�侊紝
浠ョ爺绌跺垎瀛愮殑鍚勭鎬ц川
鍜岃涓恒�?/p>
浣嗗彈鎺у垎瀛愬姩鍔涘妯℃嫙鍗磋鐢ㄤ竴涓亣鎯崇殑澶栧姏骞叉壈鎺у埗鐢熺墿澶у垎瀛愮殑琛屼负锛?/p>
杩欐槸涓?/p>
浠�涔堝憿锛?/p>
锛堥渶瑕佹煡涓�涓嬫洿澶氱殑
SMD
鐨勫簲鐢ㄥ疄渚嬶紝
璇︾粏浜嗚В
SMD
绌剁珶鍙互鐢ㄤ簬鐮旂┒浠�涔堥棶棰橈紝
鎵嶈兘鍋氬嚭鍥炵瓟锛?/p>
鍦ㄤ笅闈㈢殑渚嬪瓙涓紝鎴戜滑灏嗛鍏堝浐瀹氭硾绱犲垎瀛愪腑涓�涓師瀛愮殑浣嶇疆锛岀劧鍚庣敤涓�涓亣鎯崇殑澶?/p>
鍔涚壍鎷夊彟涓�涓師瀛愩�傜悆褰㈢殑娉涚礌鍒嗗瓙浼氬洜姝よ�岃閫愭笎鎷夊紑锛屾渶缁堟垚涓轰几灞曠姸鎬佺殑鑲介摼銆?/p>
杩涜
SMD
鏃讹紝
鎴戜滑闇�瑕佺敤宸茬粡瀹屾垚鑳介噺鏈�灏忓寲鍜岃兘閲忓钩琛★紝
杈惧埌绋冲畾鐘舵�佺殑铔嬬櫧缁撴瀯銆?/p>
濡傛灉鐢ㄥ惈鏈夋壄鏇层�?/p>
鎷変几銆?/p>
鍙樺舰鏋勮薄鐨勫師濮嬭泲鐧界粨鏋勶紝
鎴戜滑灏嗘棤娉曞垎娓呰泲鐧藉悇閮ㄥ垎鐨勮繍鍔ㄦ槸鐢?/p>
浜庤泲鐧藉唴閮ㄧ殑褰㈠彉寮犲姏寮曡捣鐨勶紝杩樻槸鐢变簬
SMD
瀹為獙闄勫姞鐨勫鍔涢�犳垚鐨勩�傚洜姝わ紝杩涜
SMD
涔?/p>
鍓嶅繀椤婚鍏堣繘琛屼竴娆″钩琛℃�佸垎瀛愬姩鍔涘妯℃嫙锛岃幏寰楃ǔ瀹氱粨鏋勩�?/p>
杩欓噷锛?/p>
鎴戜滑浣跨敤
2.4
鑺傜悆鐘舵按浣撳垎瀛愬姩鍔涘妯℃嫙杈撳嚭鐨勬仮澶嶆枃浠?/p>
锛?/p>
.restart
锛?/p>
杩涜
SMD
銆?/p>
鎭㈠鏂囦欢杈撳嚭鏃讹紝娉涚礌宸插湪姘翠綋涓畬鎴愪簡鑳介噺鏈�灏忓寲鍜岃兘閲忓钩琛★紝杈惧埌浜嗙ǔ瀹氱姸鎬併�?/p>
4.1
闄ゅ幓姘村垎瀛?/p>
涓轰簡鑺傜渷璁＄畻鏃堕棿锛?/p>
鎴戜滑鍦ㄨ繘琛屾湰娆?/p>
SMD
涔嬪墠灏嗛櫎鍘讳綋绯讳腑鎵�鏈夌殑姘村垎瀛愩�?/p>
浣嗚鑰呭繀
椤昏娉ㄦ剰锛?/p>
鍦ㄧ湡姝ｈ繘琛?/p>
SMD
瀹為獙鐨勬椂鍊欏喅涓嶅彲浠ュ皢姘村垎瀛愰櫎鍘伙紒
1
銆佹墦寮�
VMD
锛岄�夋嫨
File
鈫?/p>
New
Molecule
鑿滃崟椤癸紝杞藉叆
common
鐩綍涓嬬殑鏂囦欢
ubq_ws.psf
銆?/p>
涓嶈鍏抽棴绐楀彛锛?/p>
姝ゆ椂绐楀彛
鈥?/p>
Load file for:
鈥?/p>
涓�椤瑰簲璇ユ樉绀?/p>
鈥?/p>
0:ubq_ws.psf
鈥?/p>
銆?/p>
鍐嶆鍗曞嚮鎸夐挳
Browser
锛屾壘鍒?/p>
1-2-sphere
鐩綍涓嬬殑鏂囦欢
ubq_ws_eq.restart.coor
锛岃浇鍏?/p>
璇ユ枃浠躲�傚叧闂?/p>
Molecule File Browser
绐楀彛銆?/p>
鐜板湪鎴戜滑杞藉叆浜?/p>
2.4
鑺傜悆鐘舵按浣撳姩鍔涘妯℃嫙鏃惰緭鍑虹殑鎭㈠鏂囦欢
(.restart.coor)
銆?/p>
2
銆侀�夋嫨
Extension
鈫?/p>
tk
鑿滃崟椤癸紝鎵撳紑
tk
锛岄鍏堢敤
cd
鍛戒护鏀瑰彉褰撳墠鐩綍鑷?/p>
common
鐩綍涓嬶紝鐒跺悗杈撳叆锛?/p>
set selprotein [atomselect top protein]
$selprotein writepdb ubq_ww_eq.pdb
杩欐牱鎴戜滑渚垮湪
common
鏂囦欢澶逛笅鏂板缓浜嗕竴涓?/p>
pdb
鏂囦欢
ubq_ww_eq.pdb
锛?/p>
鍌ㄥ瓨宸茬粡杈?/p>
鍒板钩琛℃�佺殑铔嬬櫧璐ㄥ垎瀛愶紝浣嗘病鏈夋按鍒嗗瓙銆?/p>