AMBER Archive (2008)

Subject: AMBER: cis - trans isomerization

From: Nina Fischer (nfischer_at_informatik.uni-tuebingen.de)
Date: Thu Nov 27 2008 - 08:39:21 CST

Dear all,

I am trying to perform a cis->trans isomerization of PRO during a MD
simulation using AMBER 10.
Unfortunately I don't end up with the trans form of PRO in the end. I
also tried amongst others a stepwise procedure (e.g. incrementally
increasing the angle by 2° using 88 segments of 5 ps) which was also not
working. Could anyone give me a hint?

Thanks a lot in advance!

Sincerely,
  Nina

My input file (similar to the example file in the AMBER 10 manual p.109)

nstlim=100000, cut=99.0, igb=1, saltcon=0.1,
ntpr=100, ntwr=100000, ntt=3, gamma_ln=5.0,
ntx=1, irest=0, ig = 256251,
ntc=2, ntf=2, tol=0.000001,
dt=0.002, ntb=0, tempi=300., temp0=300.,
jar=1,
/
&wt type='DUMPFREQ', istep1=1, /
&wt type='END', /
DISANG=tors.RST
DUMPAVE=tors_vs_t.dump
LISTIN=POUT
LISTOUT=POUT

My tors.RST file
(produced by makeANG_RST with the following constraint: 107 PRO OMEGA
170.0 190.0):
  &rst iat = 1620, 1635, 1637, 1647,
           r1 = 169.0, r2 = 170.0, r3 = 190.0, r4 = 191.0,
           rk2 = 2.0, rk3 = 2.0, &end

My tors_vs_t.dump (output):

    170.00000 1.38157 0.20546 0.00000
    170.00000 1.38157 0.20546 -0.00035
    169.99830 0.47077 0.20656 -0.00070
    169.99660 0.08517 0.20703 -0.00105
    169.99490 0.34210 0.20672 -0.00140
    169.99320 1.25996 0.20560 -0.00175
    169.99150 2.12485 0.20454 -0.00210
    169.98980 3.49226 0.20287 -0.00245
    169.98810 4.91085 0.20114 -0.00279
    169.98640 6.09679 0.19969 -0.00313
    169.98470 7.01486 0.19857 -0.00347
    169.98300 7.60174 0.19786 -0.00381
    169.98130 7.87793 0.19752 -0.00414
    169.97960 7.62205 0.19783 -0.00448
    169.97790 6.49825 0.19919 -0.00482
    169.97620 4.31581 0.20185 -0.00516
    169.97450 1.44021 0.20535 -0.00550
    169.97280 358.57785 -0.22981 -0.00548
    169.97110 355.02320 -0.22548 -0.00510
    169.96940 350.97144 -0.22055 -0.00472
    169.96770 347.28227 -0.21605 -0.00435
    169.96600 344.66392 -0.21286 -0.00398
    169.96430 342.96674 -0.21080 -0.00362
    169.96260 342.63136 -0.21039 -0.00326
    169.96090 343.02748 -0.21088 -0.00291
    169.95920 344.48603 -0.21266 -0.00255
    169.95750 346.34113 -0.21492 -0.00218
    169.95580 348.20425 -0.21719 -0.00181
        .
        .
        .
      0.01700 13.30929 -0.01620 -13.77487
      0.01530 12.20643 -0.01485 -13.77484
      0.01360 11.51945 -0.01402 -13.77482
      0.01190 11.69342 -0.01423 -13.77479
      0.01020 12.56779 -0.01530 -13.77477
      0.00850 13.41669 -0.01634 -13.77474
      0.00680 14.71493 -0.01792 -13.77471
      0.00510 16.05183 -0.01955 -13.77468
      0.00340 16.97904 -0.02068 -13.77465
      0.00170 17.85735 -0.02176 -13.77461 

-- 
Eberhard Karls University Tübingen
Wilhelm Schickard Institut for Computer Science
Division for Simulation of Biological Systems
Room C314, Sand 14, D-72076 Tübingen

phone:	+49-7071-29-70456
fax:	  +49-7071-29-5152
email:	nfischer_at_informatik.uni-tuebingen.de
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