Dear Amber Users
I am trying to minimize my peptide in tip3pbox as demonstrated in this link
http://ambermd.org/doc6/html/AMBER-sh-4.2.html
But in the output file I am getting "Could not find cntrl namelist " (input
below) It seems to me that my input file is correct. Could any one suggest
me
whats going on.
command used:
sander -O -i min1.in -o min1.out -p prmtop_WATER -c inpcrd_WATER -r
min1.rdt -ref inpcrd_WATER
Minimization with NMR restraints:input file
===============================
PEP:Minimization protocol for water molecules and counter ions only
&cntrl
imin=1,
ncyc=50, maxcyc=1000,
nmropt=1,
ntc=2, tol=0.000001,
cut=9.0,
ntpr=100,
ntb=1,
ntr=1,
/
&wt type='REST', istep1=0,istep2=1000,value1=1.0,
value2=1.0,
/
&wt type='END'
/
LISTIN=POUT
LISTOUT=POUT
DISANG=RST_NOE_hahbhghd_hb1
Group input for restrained atoms
10.0
RES 1 20
END
END
Thanks
Vince
PS: I took best structure from GB simulates annealing and put it in TIP3PBOX
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Received on Thu Nov 05 2015 - 09:30:03 PST
