AMBER Archive (2002)

Subject: IBELLY and NMROPT in sander

From: Tom Bishop (bishop_at_tulane.edu)
Date: Thu Oct 10 2002 - 11:54:43 CDT

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
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Dept. of Environmental Health Sciences(SL-29)
School of Public Health & Trop. Medicine
1430 Tulane Avenue
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Phone: 504-988-6203   Fax: 504-585-6428 
bishop_at_tulane.edu
-----------------------------------------
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Division of Basic Pharmaceutical Sciences
College of Pharmacy
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Phone: 504-485-5106   Fax: 504-485-7954
tbishop_at_xula.edu
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