AMBER分子动力学� �例 zz
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| AMBER?????????? ?? ?????AMBER????????????????????????????????????????????????????????????????????? AMBER????????????????????University of California San Francisco,UCSF)?Peter A Kollman?????????????????????9.0?AMBER???????????????????????????????????????http://amber.scripps.edu. ???AMBER????????????? -------------------------------------------------------------------------------- Leap??????????????????????? xleap?X?windows???leap??GUI????? tleap??????Leap? Antechamber???????????????????????????Leap?????? ????????????????????antechamber??? Sander?MD????????MD????????AMBER?????? Ptraj?MD????????? -------------------------------------------------------------------------------- ???? ???????????????????oxytocin???X?????????1NPO.PDB????????????????????????????????? PDB???????????Leap????????PDB??????????????PDB?????????????????????PDB?????????????????????????????????????PDB??????????REMARKS?????????PDB????????SSBOND??????????????????????????Leap?????????????????????????oxytocin?????????????????????????????????????Linux????????Linux?????????Linux??? ?????????????? mkdir myproj cd myproj ??1NPO.PDB??????????????????PDB??????????????????????????PDB????????A?C??D?????????????oxytocin??????????oxyt.pdb??? ??Swiss PDB viewer????oxyt.pdb????????pdb??????????????Deep View?????????????????pdb???oxyt.pdb??? xleap?tleap????????????????????????????xleap????X???????tleap?????????????tleap? tleap -s -f leaprc.ff03 ??leaprc.ff03?AMBER?2003????????????????????????????????????????? oxy=loadpdb oxyt.pdb ?????oxyt.pdb???oxy???? bond oxy.1.SG oxy.6.SG ??oxy????????????SG???????????????check????oxy???????????????????�OK�?????????????????? check oxy ????????????? saveamberparm oxy oxy_vac.top oxy_vac.crd ??oxy_vac.top?oxy_vac.crd????????????????????? ??????????????? solvateoct oxy TIP3PBOX 9.0 ????Leap????TIP3PBOX???,????????9???????solvatebox?????solvatebox??????????????????????????????????8.5?????MD????????????????????????????MD????PME??????????2????cutoff?????MD??????????????????????????????? charge oxy ?????????????addions????????Cl???Na??? ????????????????????????Leap??? saveamberparm oxy oxy.top oxy.crd quit ?????????????tleap?????????????????? "oxy.leaprc" -------------------------------------------------------------------------------- source leaprc.ff03 oxy=loadpdb oxyt.pdb bond oxy.1.SG oxy.6.SG check oxy saveamberparm oxy oxy_vac.top oxy_vac.crd solvateoct oxy saveamberparm oxy oxy.top oxy.crd quit -------------------------------------------------------------------------------- ??????????????"oxy.leaprc"?????????????? tleap -s -f oxy.leaprc ??????????????????????leap.log?????Leap????????????leap??????????????????? ?????????????????????????sander????????????????????????? AMBER?????????? ??????1? ???? ??????????????NVT????????????????????????? 1????????????????????????????????????????????????????????????????????????????????????????????????????MD????????????????? Sander????????????????????????????????NMR??????????Sander????????????????????????????????????? "min_vac.in" -------------------------------------------------------------------------------- oxytocin: initial minimization prior to MD &cntrl imin = 1, maxcyc = 500, ncyc = 250, ntb = 0, igb = 0, cut = 12 / -------------------------------------------------------------------------------- Sander???????????? sander �O �i in �o out �p prmtop �c inpcrd �r restrt [-ref refc �x mdcrd �v mdvel �e mden �inf mdinfo] ???????????? sander �O �i min_vac.in �o min_vac.out �p oxy_vac.top �c oxy_vac.crd �r oxy_vacmin.rst & ????more????tail????min_vac.out????????????????? 2????????? Sander????????? md_vac.in -------------------------------------------------------------------------------- oxytocin MD in-vacuo, 12 angstrom cut off, 250 ps &cntrl imin = 0, ntb = 0, igb = 0, ntpr = 100, ntwx = 500, ntt = 3, gamma_ln = 1.0, tempi = 300.0, temp0 = 300.0, nstlim = 125000, dt = 0.002, cut = 12.0 / -------------------------------------------------------------------------------- ???? sander �O �i md_vac.in �o md_vac.out �p oxy_vac.top �c oxy_vacmin.rst �r oxy_vacmd.rst �x oxy_vacmd.mdcrd �ref oxy_vacmin.rst �inf mdvac.info & MD????????????????????????250ps???????????2?0GHz?Linux?????5??? ????????????????????sander???????????????????????sander?????????AMBER????? &ctrl?"/"?sander?????????????????????????????????????? cutoff??????????????????????????????? ntr???????????1?????0?????? imin??????????1??sander?????????0???sander?????????? macyc????????? ncyc????????????????????????????????? ntmin???????????0???10???????????????????????1??ncyc??????????????????????2?????????? dx0?????????? dxm???????? drms??????????????1.0E-4 kcal/mol.A? ???????????? AMBER?????????? ??????2? ???????????? ?????????????????????? 1???????????????????????????????????????? ???? 2???????????????????????????? 3??????????????????????????????????????0K???300K? 4???????????????????300K??????????????????????????????? ############################# 1??????????? ????????min1.in??? -------------------------------------------------------------------------------- oxytocin: initial minimisation solvent + ions &cntrl imin = 1, maxcyc = 1000, ncyc = 500, ntb = 1, ntr = 1, cut = 10 / Hold the protein fixed 500.0 RES 1 9 END END -------------------------------------------------------------------------------- ????????????500.0???kcal/mol????????????????�RES 1 9�??????????????????oxytocin?9???? ??????? sander �O �i min1.in �o min1.out �p oxy.top �c oxy.crd �r oxy_min1.rst �ref oxy.crd & 2?????????? ????min2.in??? -------------------------------------------------------------------------------- oxytocin: initial minimisation whole system &cntrl imin = 1, maxcyc = 2500, ncyc = 1000, ntb = 1, ntr = 0, cut = 10 / -------------------------------------------------------------------------------- ????? sander �O �i min2.in �o min2.out �p oxy.top �c oxy_min1.rst �r oxy_min2.rst & 3??????????? ? ???????????????????????????????????????????????????????????????????????? ???????????????????????????????10ps??????20ps?????????????????????????? ?? ??????md1.in??? -------------------------------------------------------------------------------- oxytocin: 20ps MD with res on protein &cntrl imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 10, 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 = 500, ntwr = 1000 / Keep protein fixed with weak restraints 10.0 RES 1 9 END END -------------------------------------------------------------------------------- ????????? ntb = 1????????????????? imin = 0?????????????????????? nstlim = #?????????? dt = 0.002?????????ps?0.002??2fs? temp0 = 300???????????????????K? tempi = 100?????????? gamma_ln = 1????ntt?3??????????ps-1????AMBER??? ntt = 3????????3??????????? tautp = 0.1???????????1.0????????????????? vlimit = 20.0????????????????20.0?????????????????????????????????????? comp = 44.6? ???????? ntc = 2?Shake????????1????????2?????????3????????????? tol = #.#####???????????????????? ? ?????????????10kcal/mol??????????ntr?1????????5-10kcal/mol?????????????? ?????????????????"-ref"??????????????Shake???2fs???????????????????????? ?????????????????????? ??????? sander �O �i md1.in �o md1.out �p oxy.top �c oxy_min2.rst �r oxy_md1.rst �x oxy_md1.mdcrd �ref oxy_min2.rst �inf md1.info& ??MD????????????????????????????????2.0GHz?P4???????????????????md1.in???????? 4???????????? ???????????????????????????????????????????????????????250ps?MD???????md2.in??? -------------------------------------------------------------------------------- oxytocin: 250ps MD &cntrl imin = 0, irest = 1, ntx = 7, ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0, cut = 10, ntr = 0, ntc = 2, ntf = 2, tempi = 300.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0, nstlim = 125000, dt = 0.002, ntpr = 100, ntwx = 500, ntwr = 1000 / -------------------------------------------------------------------------------- ??????????: ntb=2???????????????? ntp?1??????????????? taup = 2.0???????????ps? pres?1???1??????? ????????MD? sander �O �i md2.in �o md2.out �p oxy.top �c oxy_md1.rst � r oxy_md2.rst �x oxy_md2.mdcrd �ref oxy_md1.rst �inf md2.info & ????????P4??2.0GHz????7.5???? ? ??????????????????????????????.out??????????????????.mdcrd?????????????? ????????RMSD???????????????????????????????????????????? ??pdbviewer?? load structure??????????? ???????? ????xleap??????top crd?????ambpdb????structure?????? |
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