AMBER Archive (2003)

Subject: difference between iwrap and image?

From: yuann (yuann_at_bioinfo.ndhu.edu.tw)
Date: Sun May 11 2003 - 00:47:23 CDT

Dear all,
  Recently, I run two MD with "truncated octahedron box" solvated by
8A WATBOX216 on my B-DNA+2 drugs. The equlibrium stages include the
necessary NPT enssemble to equlibrate its density and gradually relax
the harmonic restrain on solute with increasing temperature step by step
to 300K, and finally a 2ns NPT ensemble.

The two MD are all identical but one is with iwrap=1. The two trajectories
are analyzed 1st by ptraj and then carnal. The RMSd vs time plots use
solved NMR structure as the reference structure. However I get a very
different plots between them.
The 1st with iwrap=1, http://bioinfo.ndhu.edu.tw/~yuann/TMP/2.gif
The 2nd with iwrap=0 & image, http://bioinfo.ndhu.edu.tw/~yuann/TMP/1.gif
(The image with abnormal high peak of rmsd value in '2.gif' looks like
 one drug away from DNA, and their conformations seems to be okay without
 twist)
All the cauculations use AMBER7 on AIX5.1.

Best Regards,
sychen

---------------------------------------------------------
Ptraj input of the 1st:
------------------------------------
trajin /work1/iwrap1/2ns.wat.trj.gz
trajout /work1/iwrap1/2ns.trj nobox
center :1-46
strip :WAT
strip :Na+
go

------------------------------------
Ptraj input of the 2nd:
------------------------------------
trajin /work1/iwrap0/2ns.wat.trj.gz
trajout /work1/iwrap0/2ns.trj nobox
strip :WAT
strip :Na+
center :1-46
image :1-46 familiar
go

(I also use several 'center' command to bring DNA and 2drugs back
 seprately, but the result is the same.)

------------------------------------
Carnal input:
------------------------------------
FILES_IN
  PARM p1 ./mb.top;
  STREAM s1 /work1/iwrap1/2ns.trj;
  STREAM s2 /work1/iwrap0/2ns.trj;
  STATIC s3 nmr.ref.trj;
FILES_OUT
  TABLE t1 rmsd/s1.txt;
  TABLE t2 rmsd/s2.txt;
DECLARE
  GROUP a1 (RES 1 - 46);
  RMS all1 FIT a1 s1 s3;
  RMS all2 FIT a1 s2 s3;
OUTPUT
  TABLE t1 all1;
  TABLE t2 all2;
END

----------------------------
Input of 2ns.in for SANDER:
----------------------------
2ns NPT Ensemble

 &cntrl
   imin=0, dt=0.002, ntr=0, ntb=2, nstlim=1000000,
   irest=1, ntx=7,
   ntc=2, tol=0.0000001, ntf=1,
   ntt=1, vlimit=20.0,
   ntp=1, tautp=5.0, taup=1.0,
   cut=9.0,
   ntpr=50, ntwr=50, ntwx=50,
   nscm=2500, iwrap=0,
 &end
END