转好文� amber 动力学

转好文� amber 动力学

amber ??????

1????? tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99

2??????? model=loadpdb "sbp_lin.pdb"

??crd?top?? saveamberparm model polyAT_vac.top polyAT_vac.crd

???????????

?????? addions model Na+ 0 ?????Cl-

???? solvateoct model TIP3PBOX 8.0

3???crd?top?? saveamberparm model model_wat.top model_wat.crd

4???tleap quit

5?????pdb ambpdb -p model_wat.top <> model2.pdb

6????????????????????????????????????????????

????????min1.in???

---------------------------------------------------------------------

oxytocin: initial minimisation solvent + ions ##????######

&cntrl ##??????

imin = 1, ##??????0 ??????

cut = 10 ##???????????10 ?

ntb = 1, ##?????? 0 ????1 ?? ?2 ??

maxcyc = 4000, ##????

ntr = 1, ##??????????? -ref

ncyc = 2000, ##?2000?????????????

/

Hold the protein fixed ##????

500.0 ##???????? kcal/mol

RES 1 9 ##??????? ?restrain=�:1-9�

END

END

------------------------------------------------------------------------------

???????

sander -O -i min1.in -p model_wat.top -c model_wat.crd -o min1.out -r min1.rst �ref model_wat.crd &

7?????????min2.in???min1.in????????????????

???????restrainmask=�:1-9@CA,N,C�???????????

sander -O -i min2.in -p model_wat.top -c min1.rst -o min2.out -r min2.rst&

8??????,??????

sander -O -i min3.in -p model_wat.top -c min2.rst -o min3.out -r min3.rst &

9??????????

??????????????????????????????????????????????????????????????????????????????????????????

Eq1.in ???

fix protein ,relax H2O

&cntrl

nstlim=25000, dt=0.002, ntx=1, irest=0, ntpr=500, ntwr=500,ntwx=500,

tempi=0.0,temp0=300,ntt=3, gamma_ln=1.0,

ntb=1, ntp=0,

nrespa=1,

cut = 10,

ntc=2,ntf=2,

NTR=1,

/

fix protein and HEM

10

RES 1 284

END

END

-----------------------------

nstlim = #??????????dt = 0.002?????????ps?0.002??2fs?ntx=1 irest=0 ?? ntb = 1?????????????????

imin = 0??????????????????????

temp0 = 300???????????????????K?

tempi = 100?????????? ntc=2,ntf=2 ????

gamma_ln = 1????ntt?3??????????ps-1????AMBER???

ntt = 3????????3???????????

sander -O -i eq1.in -p model_wat.top -c min3.rst -o eq1.out -r eq1.rst -ref min3.rst -x eq1.mdcrd

11??????????: eq2

-------------------------------------------------

f2:500ps MD

&cntrl

imin = 0, irest=1, ntx=5,

ntb=2, pres0 = 1.0, ntp=1,

taup = 2.0, ntc=2, ntf=2,

cut = 10, ntr = 0,

ntt = 3, gamma_ln = 1.0,

tempi = 300.0 , temp0 = 300.0

nstlim=500000, dt=0.002,

ntpr=500, ntwr=500, ntwx=500

/

----------------------------------------------------------

ntb=2????????????????Pres0?1???1???????

ntp?1???????????????taup = 2.0???????????ps?

????????MD?

sander -O -i eq2.in -p model_wat.top -c eq1.rst -o eq2.out -r eq2.rst -x eq2.mdcrd -ref eq1.rst &

?????

???????????? .rst ?.mdrcd ??????????crd????????????.gz ???gzip filename??????filename.gz ??

????????rmd?????????

ptraj xxx.top <>

xxx.in ???

trajin eq2.mdcrd.gz

trajin eq3.mdcrd.gz

trajin eq4.mdcrd.gz

trajin eq5.mdcrd.gz

rms first mass out xin.rms.dat1 :1-284@CA,C,N time 0.1

#????xin.rms.dat1??????1-284????C?N??

rms first mass out xin.rms.dat2 :88-91,172,201-204,230@CA,C,N time 0.1

#????xin.rms.dat2????????????C?N??

----------------------------------------------------------------------------

??xmgrace ???

xmgrace xin.rms.dat1 xin.rms.dat2

?????????????

ptraj xxx.top <>

xxx.in???

trajin eq7.mdcrd.gz 117 117 #eq7??117ps ???

strip :WAT #?????????????wat?top????????

strip :Na+

trajout eq7.pdb pdb nobox ????eq7.pdb.117???

-------------------------------------------

traj AR.top <<>

> trajin AR.md7.crd 300 500

> center :1-250

> image center familiar

> rms first mass out rms.dat :1-250

> average average.rst restrt

> average average.pdb pdb

> EOF

?????????sybyl??????????????????????mol2??amber?antechamber ?????

1???gaussian

* antechamber -i 49.mol2 -fi mol2 -o 49.in -fo gzmat

??????49.in??????windows?????gaussian???????????????????????????????????????????

you have Gassian output file.out (don�t forget to put some keyword in the Gassian input for the special format used by amber)

* -antechamber �i file.out �fi gout �o filr.prep �fo prepi �c resp (this step prepare the �file.prep� for your drug -c bcc all right )

* -parmchk �i file.prep �f prepi �o file.frcmod )this step prepare the file �file.frcmod�for the drug)

2? ???mol2 ?

??????sybyl ?mol2 ???

* -antechamber �i file.mol2 �fi mol2 �o filr.prep �fo prepi �c resp / -c bcc

* -parmchk �i file.prep �f prepi �o file.frcmod

now you have 2 files: file.prep and file.frcmod for the drug .

????file.prep ???????pdb????????vi prep????abc?

??pdb?prep????????,?????????

prep ?xleap???

using tleap for the protein or drug or/and complex

-xleap �s �f leaprc.ff99

-mod = loadamberparams file.frcmod

-loadamberprep file.prep

edit abc

pdb ???sybyl????vi ??pdb

-source leaprc.gaff

-RL = loadpdb file.pdb

-Solvateoct RL TIP3PBOX 10

-Addions RL Cl- 0 (0:zero for neutral charge,Cl- can be replaced by Na+)

-Saveamberparm RL fileWT.top fileWT.crd (save topology and coord. With water)

download file now