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
Received on Wed Jun 26 2002 - 22:28:21 PDT
