[AMBER] Amber

From: Shesh Nath <sheshnath65.gmail.com>
Date: Tue, 11 Jan 2011 09:49:19 +0530

Sir
  I have simulated 40-mer DNA using following NAB program.



molecule m;


m = fd_helix( "abdna", "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa", "dna" );
putpdb( "nuc20.pdb", m, "-wwpdb");


then using xleap "leaprc.ff99bsc0" I built prmtop and inpcrd files.
then I did minimization.


lastly I start heating using following step



Stage 1 heating of polyAT 0 to 50K
 &cntrl
  imin=0, irest=0, ntx=1,
  nstlim=10000, dt=0.0005,
  ntc=2, ntf=2,
  ntt=1, tautp=1.0,
  tempi=0.0, temp0=50.0,
  ntpr=50, ntwx=50,
  ntb=0, igb=0,
  cut=12.
 /


but when temperature arrise to 250K ,one strand of DNA is disappeared.
I want to my heating step is right or wrong.
     Give me suggestions








-- 
SHESH NATH
RESEARCH SCHOLAR,
THEORETICAL CONDENSED MATTER PHYSICS,
DEPARTMENT OF PHYSICS,
BANARAS HINDU UNIVERSITY,
VARANASI-221005
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Received on Mon Jan 10 2011 - 20:30:04 PST
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