[AMBER] How to turn off non-bonded interactions between non-bonded atoms?

From: Marc van der Kamp <marcvanderkamp.gmail.com>
Date: Tue, 6 Dec 2011 16:15:41 +0000

Hi there,

My question is related to a previous thread started by me:

I'd like to turn of non-bonded interactions between specific atoms. To test
if/how this works, I created a very simple test-system (where I can easily
edit the prmtop manually):
The system contains 2 Na+ and 2 Cl- ions.
My problem is that the exclusions I add don't seem to work at all, i.e. the
results/energies are identical with and without exclusions.
I've written a standard prmtop with tleap (i.e. with ions interacting with
each other), by issuing the following commands:
loadOff ions08.lib
loadAmberParams frcmod.ionsjc_tip3p
mol = loadpdb 4ions.pdb
saveAmberParm mol 4ions.prmtop 4ions.inpcrd

4ions.prmtop is attached.
I created a modified version (i.e. with all ion-ion pairs in the exclusion
list): 4ions_ex.prmtop (attached)

$ diff 4ions.prmtop 4ions_ex.prmtop
< 1 1 1 1
>        3       3       3       3
<        0       0       0       0
>        2       3       4       1       3       4        1       2       4
>        2       3
I created a inpcrd file that has one Na+ in the middle and the other 3 ions
1 Ang away from it:
$ more 4ions.inpcrd
   0.0000000   0.0000000   0.0000000   1.0000000   0.0000000   0.0000000
   0.0000000   1.0000000   0.0000000   0.0000000   0.0000000   1.0000000
Then, I started a short minimization with sander and the following min.i:
Minimization of 4 ions
ntb=0, cut=12.0,
imin=1, maxcyc=200,
This is how I ran sander, once using the prmtop without exclusions and once
$AMBERHOME/bin/sander -O -i min.i -o min.log -p 4ions.prmtop -c
4ions.inpcrd -r min.rst -ref 4ions.inpcrd
$AMBERHOME/bin/sander -O -i min.i -o min_ex.log -p 4ions_ex.prmtop -c
4ions.inpcrd -r min_ex.rst -ref 4ions.inpcrd
The result is that min.rst and min_ex.rst are identical, and the energies
etc. in min.log and min_ex.log are too. What I was hoping/expecting to see,
is that in min_ex.log VDWAALS, EEL and EAMBER would be zero (as there
shouldn't be any interactions between the 4 ions).
I have attached min.log and min_ex.log for your information.
I hope someone can tell me what is going wrong, and/or how else I could
turn of non-bonded interactions between non-bonded atoms.

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Received on Tue Dec 06 2011 - 08:30:03 PST
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