AMBER Archive (2005)

Subject: AMBER: distance restraints between two centers of mass

From: JAVIER PEREZ (javier.perez_at_uab.es)
Date: Thu May 26 2005 - 03:37:30 CDT

 Hi amber users,

I'd like to run a minimization using distance restraints. My idea is to fix
the distance between two centers of mass and then to run the minimization.

I've defined the two centers of mass and the minimization runs but it doesn
t work correctly. I check the structure of the system and I can see that the
minimization run without taking into account the distance restraints.

Next, I'll show you the files I've created for that minimization:

minimization.in

&cntrl
  imin=1, nmropt=0,
  ntx=1, irest=0, ntrx=1,
  ntb=1, igb=0, nsnb=25,
  ipol=0, gbsa=0,
  dielc=1.0, cut=8.0, intdiel=1.0,
  scnb=2.0, scee=1.2,
  ibelly=0, ntr=0,
  maxcyc=150
 &end
 &wt type='END' &end
DISANG=/disk7/xavip/irlandaII/Epotential/dist10.f
_____________________________

dist10.f

&rst
iat=-1,-1,
iresid=1,
ir6=0,
r1=0.00,
r2=10.0,
r3=10.0,
r4=50.0,
rk2=500000.0,
rk3=500000.0,
igr1=2,2,3,3,5,8,
grnam1(1)='C02', grnam1(2)='C05', grnam1(3)='C02', grnam1(4)='C05',
grnam1(5)='O2', grnam1(6)='O2',
igr2=1,1,1,1,
grnam2(1)='NP3', grnam2(2)='C06', grnam2(3)='C13', grnam2(4)='NP6',
&end

The distance I want to fix is 10 A.

I accept any suggestion.

Thanks in advance

Javier

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