Amber网上教程地址 zz
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| http://www.rosswalker.co.uk/tutorials/amber_workshop/ http://amber.scripps.edu/tutorials/ amber8/9 http://amber.scripps.edu/dbase.html amber ff in gmx http://folding.stanford.edu/ffamber/ other http://www.chpc.utah.edu/%7Echeatham/software.html AMBER ????SMD?? ????????AMBER????( umbrella.RST # Change distance between atoms 1771 and 3787 from 63 A to 253 A &rst iat=1771,3787,r1=10., r2=63.,r3=63.,r4=210.,rk2=10.,rk3=10., / smd.in Sample pulling input &cntrl nstlim=1000000, cut=99.0, igb=1, saltcon=0.1, ntpr=10, ntwr=10, ntt=3, gamma_ln=5.0, ntx=5, irest=1, ntwx=10, ig = 256251, ntc=2, ntf=2, tol=0.000001, dt=0.002, ntb=0, tempi=310., temp0=310., jar=1, / &wt type=DUMPFREQ, istep1=1, / &wt type=END, / DISANG=dist.RST DUMPAVE=dist_vs_t LISTIN=POUT LISTOUT=POUT amber???????? ???????????amber, ???, ?? ?????????????????????????????????????????????????????????????????????????????????????????amber??antechamber ?????????????????????????????????antechamber????mopac???????gaussian????????gaussian?????? ???????sybyl??????????????gaussian??????????????????????????gaussian??????????antechamber????????????????????????? ?????????????mol2????????????antechamber????gaussian?????????? antechamber -i 49.mol2 -fi mol2 -o 49.in -fo gzmat ??????49.in??????windows?????gaussian???????????????????????????? ??????????????? ??????49.out??????????????antechamber?????????? antechamber -i 49.out -fi gout -o 49mod.mol2 -fo mol2 -c resp ????????????mol2?????????????????????????????????mol2????? ???????????????????????????????????????????gaff??????????? ????? parmchk -i 49mod.mol2 -f mol2 -o 49mod ????????????49mod?????? ??????????? amber???leap?????????????????PDB????????????????????????????????? PDB????????????????????????????????????????????????????????? ???????????????????? ATOM 12 1H ARG A 82 12.412 8.891 34.128 1.00 0.00 H ?PDB??????????????13??14???H???????grep?????13??14???H?? ????? grep -v ^.............H 1t4j.pdb > x grep -v ^............H x > 1t4j_noh.pdb ???????????????????????????????????????????????????????? ????????????????????????????????????????????????leap??? ???????????????????????????????????????? ??????????????????????????????????????????????????????unit????? ?????????????????????????????????????????CYX?????CYS ????????????????????????????????????????? ???????????????????????????????????????PDB???????????????????? antechamber ???49mod.mol2??????????????leap??????????????????????????? ???????????????????????? ????????????????49mod.mol2??????????????????????????????????? ???????????????????????????????????????????????????????? ?????????????? ???????????????????????????????????????????????????????????? ??????? ???????????????????????? ??????????????? ?amber?????????????????????????????????????????????????????? ?????????????????????leap ????? amber????leap????????????tleap???????????Xleap???amber????????????????? ?????????????????????tleap???leap????????????????????? ??tleap??shell?????tleap?leap?????shell???? -I: Adding /usr/local/amber8/antechamber-1.23/dat/leap/prep to search path. -I: Adding /usr/local/amber8/antechamber-1.23/dat/leap/lib to search path. -I: Adding /usr/local/amber8/antechamber-1.23/dat/leap/parm to search path. -I: Adding /usr/local/amber8/antechamber-1.23/dat/leap/cmd to search path. Welcome to LEaP! (no leaprc in search path) > ??>?leap???? ?????????amber????????????????????????????????amber???????????? ???????????leap???????????? amber???????????????????gaff?02??????? >source leaprc.gaff >source leaprc.ff02 ??????????? ?????list??????????? ????????????unit???20????????????????????? ??????????????????????????? >loadamberparams 49mod ????????,????? >MOL = loadmol2 49mod.mol2 ??MOL?unit????????????pdb????????????????????????pdb??????? ?????list????????????unit: ??????????? ????pdb???????? >comp = loadpdb 1t4j_noh.pdb ??????????????????????unit??atom?????????????????pdb????????? ?????????????????????????????????????????? Creating new UNIT for residue: FRJ sequence: 1 Created a new atom named: O36 within residue: .R Created a new atom named: S33 within residue: .R Created a new atom named: O35 within residue: .R Created a new atom named: N34 within residue: .R ???????????????????PDB????????????leap????????????????????? ?????????? Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A ??????????????????CYX???????????????????????????????????? ??bond?????????????? >bond comp.35.SG comp.179.SG ??comp???????????35?179??????SG?CYX?????????????comp.35.SG????????? ????? ???????????????????????????????????????????????? >solvatebox comp TIP3PBOX 10.0 solvatebox?????????????????comp????????TIP3PBOX??????????10.0??????? ?????????0????????????????????????????????????????????????? >addions comp Na+ 0 ??????????????????????????????? ????????????????????????????????????????????leap?????????? ??????????????????????????????? >saveoff comp 1taj.off ????????off??????????????????? >saveamberparm comp 1t4j.prmtop 1t4j.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 1 improper torsion applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these dont have chain types marked: res total affected CMET 1 ) (no restraints) >quit ?????????????????????????????????????????????ambpdb??????? ?pdb?????????????????????? [snowyowls@localhost actualamber]$ ambpdb -p 1t4j.prmtop <1t4j.inpcrd> kankan.pdb | New format PARM file being parsed. | Version = 1.000 Date = 09/08/06 Time = 16:36:09 [snowyowls@localhost actualamber]$ ?????????????????????????????????????????? ???????? ?amber???????????????????????????????????1t4j.prmtop ?1t4j.inpcrd???? ????????????????????? ???????????????????????????????????????????????????????? ??????????????????????????????????????? ?????sander???????sander????????????????????????????sander?????? ????????????????????????????min_1.in Initial minimisation of our structures &cntrl imin=1, maxcyc=4000, ncyc=2000, cut=10, ntb=1,ntr=1, restraint_wt=0.5 restraintmask=:1-283 / ???????????????????? &cntrl?/??????????? ??imin=1??????????maxcyc=4000?????????4000??ncyc=2000??????????4000??? ? 2000??????????2000????????????????????????????????????? ????NTMIN???NTMIN =0???????????NTMIN=2???????????????=3?=4???????xmin??lmod? ??????????? ????cut=10?????????????????? ntb=1?????????????????????????????????? ???????????????????ntb=1???????????????ntb=0?ntr=1??????????????????? ?????????????? ???????????????????restraint_wt=0.5???????????????????????????????? ???????????????????????????????????????????????????????????? Kcal/(mol*A)? restraintmask=:1-283???????1?283???????????1-283????????????????284 ??????????????????????????????????????????????????tleap??????? ????????????? ????sander???????? [snowyowls@localhost actualamber]$ sander -O -i min_1.in -p 1t4j.prmtop -c 1t4j.i npcrd -ref 1t4j.inpcrd -r 1t4j_min1.rst -o 1t4j_min1.out ????-O???????????-i min_1.in??sander??????min_1.in?-p 1t4j.prmtop????????? ?-c 1t4j.inpcrd???????-ref 1t4j.inpcrd?????????????????????ntr=1??????? sander??-ref???????????????- ref 1t4j.inpcrd????1t4j.inpcrd???????????????? ???????????-r 1t4j_min1.rst??????????????????1t4j_min1.rst????-o 1t4j_min1.out ??????????????????1t4j_min1.out???? ????????????? 1t4j_min1.rst????????????????????????????????????? ???????????????????min_2.in ?min_3.in min_2.in Initial minimisation of our structures &cntrl imin=1, maxcyc=5000, ncyc=2500, cut=10, ntb=1,ntr=1, restraint_wt=0.5 restraintmask=:1-283@CA,N,C / ????????????????? :1-283@CA,N,C??1-283??????CA?N?C?????????????????? ????????????????????????????????????????????? min_3.in Initial minimisation of our structures &cntrl imin=1, maxcyc=10000, ncyc=5000, cut=10, ntb=1, / ????????????????????????????? ?????????? [snowyowls@localhost actualamber]$ sander -O -i min_1.in -p 1t4j.prmtop -c 1t4j.inpcrd -ref 1t4j.inpcrd -r 1t4j_min1.rst -o 1t4j_min1.out [snowyowls@localhost actualamber]$ sander -O -i min_2.in -p 1t4j.prmtop -c 1t4j_min1.rst -ref 1t4j_min1.rst -r 1t4j_min2.rst -o 1t4j_min2.out [snowyowls@localhost actualamber]$ sander -O -i min_3.in -p 1t4j.prmtop -c 1t4j_min2.rst -r 1t4j_heat0.rst -o 1t4j_min3.out ????????????????�� |
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