Dear amber,
Is ibelly=1 and nmropt=1 a valid combination in sander for amber7?
In particular I'm having problems with the following input file (3
versions attached as follows)
Sander runs with ibelly = 0 and nmropt = 1
and Sander runs with ibelly=1 and nmropt =0 (if I remove the &wt,
DISTANG, and LISTOUT lines)
But to get ibelly=1 and nrmopt=1 to run I have to move the
section 8 lines that define the GROUP INFORMATION
to the beginning of the input file and leave the DISTANG and LISTOUT
lines in place directly after the &cntrl information.
The &wt information can be placed anywhere.
It seems the read for &wt namelist information that is triggered by
nrmopt=1 "rewinds" the file to the beginning once it is finished
If this is the "proper" behavior then a more careful description of the
interrelationship between the different "sections"
as described on page 83 of the amber7 manual and namelist information
would be greatly appreciated.
Thanks,
TOm
*********** input file for running ibelly=1 and
nmropt=1**********************
Title LIG
FIND
* * * LIG
SEARCH
RES 1 999
END
Title WAT
FIND
* * * WAT
SEARCH
RES 1 999
END
END
# Minimization
&cntrl
ibelly =1,
maxcyc=1000, imin =1, cut =12.0
ntb=0, ntc =1, ntf=1, tol=0.00001,
igb =0,
ntpr =100, ntwx = 500,ntwe=500,
dxm = .01, NMROPT = 1,
&end
LISTOUT=POUT
DISTANG=RST
&wt type='NB', istep1=0, istep2=500,
value1=0.0, value2=1.0, &end
&wt type='END' &end
***************************************************
*********** input file for running ibelly=1 and
nmropt=0**********************
# Minimization
&cntrl
ibelly =1,
maxcyc=1000, imin =1, cut =12.0
ntb=0, ntc =1, ntf=1, tol=0.00001,
igb =0,
ntpr =100, ntwx = 500,ntwe=500,
dxm = .01, NMROPT = 0,
&end
Title LIG
FIND
* * * LIG
SEARCH
RES 1 999
END
Title WAT
FIND
* * * WAT
SEARCH
RES 1 999
END
END
***************************************************
*********** input file for running ibelly=0 and
nmropt=1**********************
# Minimization
&cntrl
ibelly =0,
maxcyc=1000, imin =1, cut =12.0
ntb=0, ntc =1, ntf=1, tol=0.00001,
igb =0,
ntpr =100, ntwx = 500,ntwe=500,
dxm = .01, NMROPT = 1,
&end
&wt type='NB', istep1=0, istep2=500,
value1=0.0, value2=1.0, &end
&wt type='END' &end
LISTOUT=POUT
DISTANG=RST
Title LIG
FIND
* * * LIG
SEARCH
RES 1 999
END
Title WAT
FIND
* * * WAT
SEARCH
RES 1 999
END
END
--
-----------------------------------------
Thomas C. Bishop, Ph.D.
Joint Faculty Appointments Program Professor
Center for Bioenvironmental Research
-----------------------------------------
Tulane University Office
-----------------------------------------
Dept. of Environmental Health Sciences(SL-29)
School of Public Health & Trop. Medicine
1430 Tulane Avenue
New Orleans, LA 70112
Phone: 504-988-6203 Fax: 504-585-6428
bishop_at_tulane.edu
-----------------------------------------
Xavier University Office
-----------------------------------------
Division of Basic Pharmaceutical Sciences
College of Pharmacy
7325 Palmetto Street
New Orleans, LA 70125
Phone: 504-485-5106 Fax: 504-485-7954
tbishop_at_xula.edu
-----------------------------------------
Received on Thu Oct 10 2002 - 09:54:43 PDT
