AMBER Archive (2006)

Subject: AMBER: MD with restraint (nmropt=1)

From: a a (patd_2_at_hotmail.com)
Date: Tue Dec 05 2006 - 02:11:38 CST

Dear Amber users,

I could like to run a minization and MD calculation with six hydrogen bond
restrainted. they are

(residue 4, atomname H61)........(residue 1, atomname O4)
(residue 4, atomname N1)...........(residue 1, atomname H3)
(residue 4, atomname H2)...........(residue 1, atomname O2)
(residue 3, atomname H41).........(rsidue 2, atomname O6)
(residue 3, atomname N3)...........(residue 2, atomname H1)
(residue 3, atomname O2)............(residue 2, atomname H21)

Remarks: I copy the atomname name from the xleap windows when I selected
those atoms and chose "edit selected atom".

It is the input file that I used:

Initial minimisation of our complex
&cntrl
  imin=1, maxcyc=500, ncyc=200, ntr=0,
  cut=16, ntb=0, igb=1, nmropt=1
&end
&wt type = "END"&end
DISANG=./DISANG.rst
/

It is the DISANG.rst file used:

# distance restraints
&rst iat=-1, iresid=1, 2, 3, 4
IALTD=1
    r2=2.0, r3=5.0, r4=10.0
    igr1 = 1,2,3,4,
GRNAM1(1)=h3, GRNAM1(1)=o4, GRNAM1(1)=o2
GRNAM1(2)=o6, GRNAM1(2)=h1, GRNAM1(2)=h21
GRNAM1(3)=h41, GRNAM1(3)=n3, GRNAM1(3)=o2
GRNAM1(4)=h61, GRNAM1(4)=n1, GRNAM1(4)=h2
&end

I did not get the work done at all, could you mind to help and point out
what is wrong with these input files?

Best regards,
Annie

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