Dear Amber List members,
I have combined in productive MD distance and torsion restraint in md4.in
script. The latter calls RST.dist and rst.bb files. The calculation is
conducted by amber 14 with ff14sb force field in periodic water box.
Unfortunately the torsion restraint doesn't work. I think there is an error
in md4.in call of rst.bb file.
I am a new amber user and I would appreciate your advise how to correct my
script.
Thank you,
Michael
*md4.in <
http://md4.in>*
30 ns production phase MD
&cntrl
imin = 0, irest = 1, ntx = 5,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 1.0,
cut = 10.0, ntr = 0, iwrap = 1,
ntc = 2, ntf = 2,
tempi = 310.0, temp0 = 310.0,
ntt = 3, gamma_ln = 0.5,
nstlim = 15000000, dt = 0.002,
ntpr = 5000, ntwx = 5000, ntwr = 5000, ig = -1,
nmropt=1,
/
&wt type='END' /
DISANG= ../RST.dist
LISTOUT=POUT
/
DISANG1= ../rst.bb
LISTOUT=POUT
/
*RST.dist*
&rst
ixpk= 0, nxpk= 0, iat=1030,1692, r1= 1.30, r2= 1.80, r3= 2.80, r4= 3.30,
rk2=50.0, rk3=50.0, ir6=1, ialtd=0,
&end
&rst
ixpk= 0, nxpk= 0, iat=1030,61, r1= 1.30, r2= 1.80, r3= 3.00, r4= 3.50,
rk2=50.0, rk3=50.0, ir6=1, ialtd=0,
&end
*rst.bb <
http://rst.bb>*
&rst
iat=36,51,53,55, r1=0., r2=180., r3=180., r4=360.,
rk2 = 35., rk3 = 35., /
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: michael.shokhen.gmail.com
email: shokhen.mail.biu.ac.il
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Received on Mon Jul 27 2015 - 06:30:02 PDT
