AMBER Archive (2008)

Subject: AMBER: distance restraint in minimization

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Tue Dec 16 2008 - 16:44:35 CST

Hi,
I modified the pdb file and the fixbond to be DT, and i have the
following input file

CEBP8 minimization of 20,000 steps
&cntrl
imin = 1,
maxcyc = 20000,
ncyc = 10000,
ntb = 1,
ntr = 0,
cut = 10,
nmropt = 1,
/
&wt type='REST’, istep1=0,istep2=5000,value1=0.1,value2=4.0, /
&wt type=’REST’, istep1=5001,istep2=20000,value1=4.0,value2=4.0, /

&wt type=’END’ /
DISANG = RST.f

if i try and run this locally just to see if it runs
> sander -O -i minimize.in -o CEBP8.out -c CEBP8.inpcrd -p CEBP8.prmtop
-r CEBP8.rst
i get > At line 841 of file _nmrcal.f
Fortran runtime error: End of file

a copy of RST.f is below

# 11 ASN ND2 142 DT O4 2.5
&rst
ixpk= 0, nxpk= 0, iat= -1,2838, r1= 1.30, r2= 1.80, r3= 2.81, r4= 3.31,

rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
igr1= 180, 181,
&end
#
# 11 ASN ND2 143 DT O4 5.5
&rst
ixpk= 0, nxpk= 0, iat= -1,2870, r1= 1.30, r2= 1.80, r3= 6.17, r4= 6.67,
igr1= 180, 181,
&end
#
# 69 ASN ND2 121 DT O4 2.5
&rst
ixpk= 0, nxpk= 0, iat= -1,2171, r1= 1.30, r2= 1.80, r3= 2.81, r4= 3.31,
igr1=1179,1180,
&end
#
# 69 ASN ND2 122 DT O4 5.5
&rst
ixpk= 0, nxpk= 0, iat= -1,2203, r1= 1.30, r2= 1.80, r3= 6.17, r4= 6.67,
igr1=1179,1180,
&end
~

I am not sure if this is a syntax error or not. Also would this run on
AMBER 9?

Best wishes,
Taufik
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