AMBER Archive (2008)

Subject: AMBER: hydrogens are flying in replica exchange simulations

From: Ashish Sangwai (ashishsangwai_at_gmail.com)
Date: Fri Apr 18 2008 - 18:43:01 CDT

Hello,

I am trying to carry out replica exchange simulation on polyalanine (5 mer)
system in Generalized Born solvent.

For replicas above 440 K, the hydrogens in the system are having unbound
co-ordinates.

My input file looks like :

 &cntrl
   imin=0, ntx=5, irest=1, ntxo=1, ntpr=500, ntwr=500, ntwx=200,
   ntwe=500, ntf=2, ntb=0, igb=5, nstlim=10000,
   temp0 = 300, tempi=300, ntt=2, tautp=1.0,
   ntp=0, cut=999.0, saltcon=0.001,
   taup=2.0, ntc=2, ntrx=1,
   dt=0.001, ig=323657, numexchg=500,
 &end
END

System was prepared in xleap with following commands :

source leaprc.ff03
set default PBradii mbondi2
1a = sequence {ALA ALA ALA ALA ALA}
saveamberparm 1a 1a.prmtop 1a.inpcrd

In the most recent PDB file of REM simulation, hydrogen co-ordinates are
unbound.....

This PDB was generated after 38 exchange attempts for a replica at 440 K.
Rest of the backbone is still bound .

REMARK ALA
ATOM 1 N ALA 1 4.380 1.257 0.972
ATOM 2 H ALA 1 117.737 228.487 148.973
ATOM 3 CA ALA 1 5.181 0.081 0.806
ATOM 4 HA ALA 1 -8.373 -76.768 181.924
ATOM 5 CB ALA 1 4.404 -0.715 -0.190
ATOM 6 1HB ALA 1 -94.721 143.367-170.150
ATOM 7 2HB ALA 1 258.561-362.545-208.892
ATOM 8 3HB ALA 1 -121.572 -49.341 56.075
ATOM 9 C ALA 1 6.711 0.289 0.471
ATOM 10 O ALA 1 7.423 -0.676 0.212
ATOM 11 N ALA 2 7.223 1.533 0.473
ATOM 12 H ALA 2 -125.699 177.403 48.942
ATOM 13 CA ALA 2 8.634 1.801 0.462
ATOM 14 HA ALA 2 169.270-226.264-215.241
ATOM 15 CB ALA 2 9.010 3.115 -0.180
ATOM 16 1HB ALA 2 -311.134 87.755-407.032
ATOM 17 2HB ALA 2 -64.133 420.606 351.098
ATOM 18 3HB ALA 2 355.577 -48.094-155.287
ATOM 19 C ALA 2 9.323 1.628 1.800
ATOM 20 O ALA 2 8.714 1.354 2.846
ATOM 21 N ALA 3 10.639 1.796 1.792
ATOM 22 H ALA 3 55.123 15.439-100.645
ATOM 23 CA ALA 3 11.555 2.060 2.927
ATOM 24 HA ALA 3 -216.220 363.839 259.284
ATOM 25 CB ALA 3 11.623 0.734 3.689
ATOM 26 1HB ALA 3 155.952-122.441 -95.372
ATOM 27 2HB ALA 3 79.353 44.635 188.102
ATOM 28 3HB ALA 3 -407.256-128.682 -6.444
ATOM 29 C ALA 3 12.963 2.618 2.563
ATOM 30 O ALA 3 13.929 2.618 3.318
ATOM 31 N ALA 4 13.114 3.032 1.325
ATOM 32 H ALA 4 12.399 2.677 0.706
ATOM 33 CA ALA 4 14.191 3.898 0.745
ATOM 34 HA ALA 4 15.133 3.670 1.244
ATOM 35 CB ALA 4 14.334 3.685 -0.741
ATOM 36 1HB ALA 4 80.378-330.692 -73.240
ATOM 37 2HB ALA 4 13.457 4.049 -1.277
ATOM 38 3HB ALA 4 15.200 4.236 -1.108
ATOM 39 C ALA 4 13.926 5.388 1.011
ATOM 40 O ALA 4 14.864 6.200 1.003
ATOM 41 N ALA 5 12.739 5.814 1.451
ATOM 42 H ALA 5 12.045 5.089 1.560
ATOM 43 CA ALA 5 12.360 7.109 2.018
ATOM 44 HA ALA 5 13.242 7.714 2.229
ATOM 45 CB ALA 5 11.627 7.902 0.925
ATOM 46 1HB ALA 5 10.831 7.360 0.413
ATOM 47 2HB ALA 5 11.254 8.883 1.220
ATOM 48 3HB ALA 5 12.343 8.027 0.113
ATOM 49 C ALA 5 11.526 6.921 3.332
ATOM 50 O ALA 5 10.378 7.256 3.490
TER
END

Groupfile :

-O -i inp.300 -p 1a.prmtop -c restrt.300 -r r1.300 -o out.300 -rem 1 -x
mdcrd.300
-O -i inp.320 -p 1a.prmtop -c restrt.320 -r r1.320 -o out.320 -rem 1 -x
mdcrd.320
-O -i inp.340 -p 1a.prmtop -c restrt.340 -r r1.340 -o out.340 -rem 1 -x
mdcrd.340
-O -i inp.360 -p 1a.prmtop -c restrt.360 -r r1.360 -o out.360 -rem 1 -x
mdcrd.360
-O -i inp.380 -p 1a.prmtop -c restrt.380 -r r1.380 -o out.380 -rem 1 -x
mdcrd.380
-O -i inp.400 -p 1a.prmtop -c restrt.400 -r r1.400 -o out.400 -rem 1 -x
mdcrd.400
-O -i inp.420 -p 1a.prmtop -c restrt.420 -r r1.420 -o out.420 -rem 1 -x
mdcrd.420
-O -i inp.440 -p 1a.prmtop -c restrt.440 -r r1.440 -o out.440 -rem 1 -x
mdcrd.440

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu