AMBER Archive (2005)

Subject: AMBER: &dipoles in sander

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Fri Jan 21 2005 - 05:59:47 CST


Dear amber members,

I use amber8.
I would like to utilize &dipoles option
for a small charged molecule in polarized water.
However, I keep getting errors messages with sander
when I turn on the &dipoles option.
I was wondering how one can define a charged amino
group of a solute
with &dipoles parameter in an input file to run
sander.

Here are the steps that I have taken to run sander

Firstly, I prepared my prmtop and incrd files in tleap

tleap
source leaprc.ff02
source leaprc.gaff
mol=loadmol2 mol.mol2
solvateoct mol2 POL3BOX 10
saveamberparmpol mol2 mol.prmtop mol.x
quit

Secondly, I relaxed water molecules in my solvated
system
putting a restrain on my solute as follows,

input1:
 
 &cntrl
 imin=1, maxcyc=200,
 ntpr=5,
 ntr=1,
 ipol=1,
 &end
Group input for restrained atoms
100.0
RES 1
END
END

sander -O -i input1 -o output1 -p mol.prmtop -c mol.x
/
-ref mol.x -r mol.relaxed.x

After relaxing polarized water molecules, I re-ran
sander
this time adding &dipoles option in my input file for
a charged amino group as follows,

input2 :

 &cntrl
 imin=1, maxcyc=1,
 ntpr=1,
 ntr=1,
 ipol=1,
 /
 &dipoles
 NEA.1.N6
 &end
Group input for restrained atoms
100.0
RES 1
END
END

sander -O -i input2 -o output2 -p mol.prmtop -c
mol.relaxed.x -ref mol.relaxed.x

However , I got this error message in the output file

.
.
.
 5. REFERENCE ATOM COORDINATES

  NEA
    ----- READING GROUP 1; TITLE:
  &dipoles
                      

     GROUP 1 HAS HARMONIC CONSTRAINTS 16.38500

     rfree: Error decoding variable 2 2 from:
Group input

     this indicates that your input contains

      incorrect information

     field 2 was supposed to

      have a (1=character, 2=integer, 3=decimal) value

Because I have not found a sample input for measuring
polarizable potentials of certain atom groups in
solvated
systems neither in turorial nor in the manual, I have
decided
to e-mail amber folks hoping that someone could
possibly
remedy input2.

best regards,

jenk.

                
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