[AMBER] Pmf ....restrain

From: Rasha Alqus <rasha.alqus.manchester.ac.uk>
Date: Wed, 26 Feb 2014 11:29:02 +0000

Dear Amber useres,

  I want to perform PMF calculation for my system using distance restrain, and additional harmonic restrain on complex B .
In the input file if i used only one restrain highlighted in red or green , the job finish normally , but when i combine the two restrain the job fail. Can you advise me on how to write the input file with two restrain.

imin = 0,
 ntx = 1,
 irest = 0,
 ntpr = 5000,
 ntwr = 50000,
 ntwx = 10000,
 ntrx = 1,
 ntxo = 1,
 ntwv = 0,
 ntf = 2,
 ntc = 2,
 cut = 999,
 igb = 0,
 ntb = 0,
 nstlim = 500000,
 dt = 0.002,
 tempi = 300.0,
 temp0 = 300.0,
 ntt = 3,
 gamma_ln = 1.0,
 ntp = 0,
 taup = 0.50,
 nmropt = 1,
 ioutfm = 1,
 ig = -1,
 ntr = 1,
 /
Hold the B complex fixed
200
ATOM 1 1094
END
END
/
&wt type='END',
 /
DISANG=dist.RSTRAIN
/


Many thanks for help in advance
Regard
R.W




The dist.restrain file is
&rst

iat=-1, -1
igr1=531,556,561,560,535,534,
igr2=1095,1096,1097,1098,1099,1100,1101,1102,1103,1104,1105,1106,
r1=0, r2=5, r3=5, r4=99,
rk2 =5, rk3 = 5,
/




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Received on Wed Feb 26 2014 - 03:30:02 PST
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