AMBER Archive (2009)

Subject: [AMBER] steps for NMR structure minimization of protein

From: Prem Prakash Pathak (prempolymer_at_gmail.com)
Date: Mon Jun 29 2009 - 09:12:40 CDT

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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