Re: [AMBER] Help needed regarding simulating Lipopolysaccharide

From: David A Case <>
Date: Mon, 17 Aug 2015 07:49:21 -0400

On Mon, Aug 17, 2015, Mrinda Jones wrote:
> I am trying to simulate the Lipopolysaccharide molecule of 271 atoms. The
> initial structure was drawn and saved in the .pdb format which stays as the
> input file for the simulation (attached herewith).

What force-field are you using? The fact that you are getting large values
for the 1-4 EEL term suggests that you may have hydroxyl hydrogens that have
zero LJ parameters, and which are getting too close to other atoms.

This is likely to involve the hydrogens attached to the phosphate oxygens.
Are you sure that you want those phosphate groups to be doubly protonated?
That would likely occur only under very acidic conditions.

Even if you go back to the singly protonated versions, which should be stable
under mildly acidic conditions, you probably need to use higher force
constants for the phosphate group to prevent these sorts of instabilities
(assuming the problem does lie within the phosphate groups.) See the comments
in the frcmod.phosaa10 file in $AMBERHOME/dat/leap/parm.

You can find out more by using the "checkValidity" command in parmed, using
the structure after 500 steps of minimization or so.


AMBER mailing list
Received on Mon Aug 17 2015 - 05:00:06 PDT
Custom Search