AMBER Archive (2002)

Subject: Problem in amber

From: Monica (monicdbs_at_iitr.ernet.in)
Date: Thu Jun 27 2002 - 00:28:21 CDT

Dear AMBER users,

i am running restrained molecular dynamics protocol on DNA hexamer with
NMR restraints in presence of water and counterions on AMBER6.First I
tried to minimize water and ions using following input file:
 **********************************************************
Here is my input File:
minimization for cgatcg using abc.top and abc.crd
 &cntrl
       imin=1, ncyc=50, maxcyc=1000, nmropt=1, ntc=2, tol=0.000001, cut=9,
       ntpr=100, ntb=1, ntr=1, scee=1.2,
 &end
 &wt type='REST', istep1=0,istep2=2000,value1=1.0,
            value2=1.0, &end
 &wt type='END' &end
LISTOUT=POUT
DISANG=pamitaout.dist

Group input for restraint atom
  10.0
RES 1 12
END
END
*********************************************************
I am getting the following errorin my output file:

 1. RESOURCE USE:
 getting box info from bottom of parm
 getting new box info from bottom of inpcrd | peek_ewald_inpcrd: Box info
not found in inpcrd
   EWALD SPECIFIC INPUT:
 -------------------------------------------------
 NO EWALD INPUT FOUND: USING DEFAULTS
 -------------------------------------------------
     Largest sphere to fit in unit cell has radius = 0.000
 Ewald PARAMETER RANGE CHECKING:
 parameter skinnb+cutoffnb: (nonbond list cut) has value 0.10000E+02
 This is outside the legal range
 Lower limit: 0.00000E+00 Upper limit: 0.00000E+00
 Check ew_legal.h
*************************************************
I will be grateful if anyone could suggest reason for the above error

Thankyou in advance

Monica ( Research Scholar)
Deptt Biosci Biotech
IIT. Roorkee
India