Dear All, i wanted to minimize my NMR structure of protein of 15 kDa using
AMBER9
i have followed, following steps. is it right
step 1. Prepration of pram file with solvent box of 12 force field
leaprc.ff99SB
step 2. Minimization of solvent with nmr constraints
&cntrl
imin=1, nmropt=1, pencut=-1.0, maxcyc=1000, ncyc=500,
ntb=1, ntr=1, cut=12
ntpr=100,
&end
/&wt type='REST', istep=1.istep2=0, value1=1.0, value2=1.0, /
&wt type='END' /
DISANG=RSTPF
LISTOUT=POUT
Hold the adf fixed
500.0
RES 1 140
END
END
step 3. Minimization of protein
&cntrl
imin = 1,
maxcyc = 5500,
ncyc = 1000,
ntb = 1,
ntr = 0, ((((((( putting ntr=0 Ok.)))) ntr=1 gives problem here i do
not know why
cut = 12,
nmropt=1,
/
/&wt type='REST', istep=1.istep2=0, value1=1.0, value2=1.0, /
&wt type='END' /
DISANG=RSTPF
step 4. MD run for 5ps
step 5. repeat the step 2 and 3 of minimization using the out put coordinate
of the step 5 for MD of 5ps.
so apart form mdcrd file what more i need for analysisng the out put for
salt bridge and rmsf values?
Thanking you all in anticipation
Prem
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Received on Mon Jul 06 2009 - 12:13:20 PDT
