Dear Amber Users
I want to simulate the neat SPC/E water in a box. So for this I pack few
water molecules in packmol and run the tleap to generate topology and crd
file.
I have given the following leap command and run by tleap -s -f leap.in
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
source leaprc.ff99bsc0
WAT = SPC
HOH = SPC
loadAmberParms frcmod.spce
set SPC.1 name "SPC"
set default FlexibleWater on
RM = loadpdb wat_pack.pdb
set RM box {25.7 25.7 25.7}
check RM
charge RM
savepdb RM watSPC.pdb
saveAmberParm RM watSPC.top watSPC.crd
quit
''''""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
By searching SPC/E water model parameter in topology file, I found that the
leap taken the default TIP3P water model parameter.
#####################
Topology file
#####################
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
*5.53000000E+02 5.53000000E+02*
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
*1.51360000E+00 9.57200000E-01*
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
1.00000000E+02
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
1.82421892E+00
...................................
.....................................
FLAG SOLTY
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
5.81935564E+05 0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
5.94825035E+02 0.00000000E+00 0.00000000E+00
Please guide me where I am doing mistake to assign the SPC/E water
parameter?
Thank you in advance for your consideration.
Rahman
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Received on Wed Mar 26 2014 - 11:30:02 PDT
