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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Received on Fri Jan 21 2005 - 12:53:00 PST
