AMBER: Topology file problem in TI !

From: Pradipta Bandyopadhyay <>
Date: Wed, 7 Mar 2007 16:38:39 +0530 (IST)

Dear All,

This is regarding the topology and coordinate file preparation for TI

  I am using AMBER 8 in a linux machine.

  I am mutating ILE to VAL. More specifically the following atoms are mutated

  HD11 Dummy
  | |
  | |
  CD1---HD12 ---> HG--Dummy
  | |
  | |
  HD13 Dummy

  i.e. all delta H of ILE are converted to dummy in VAL and delta C of ILE
is converted to one gamma H in VAL.

  I plan to do both electrostatic and VDW in one step for this model system.
 This is what I did in xleap

  source leaprc.ff99
  edit ILE

  after that the charges of ILE atoms are changed to the charges of the
VAL atoms. Interestingly

  charge ILE.1.CA

  gives same charge for CA for both unperturbed and perturbed states.

  desc ILE.1.CA

gives correct charge for unperturbed but gives the delta
charge for perturbed state instead of the perturbed state though it says
perturbed charge (this may be what amber8 manual in page 33 and 34 says -
so probably this is fine).

  The problem comes with the CD1(atom type CT in ILE). In the perturbed
state, its charge should 0.0791 - I put the delta charge accordingly.

  However, as long as I keep its type as CT in the perturbed state (same
as in the unperturned state, ILE), it is fine.

  charge ILE

  gives charge 0.0 for both unperturbed and perturbed states.

However, since it is not CT, I need to change it.

 As soon I change it, charge of VAL becomes non-integral (it is becoming
-0.0791 i.e. it is not reading the charge of CD1 in the perturbed state).


 desc ILE.1.CD1 gives

 correct unperturbed and delta charge (though it says 'Perturbed charge')
Can anyone help me with this?

 Do I need to define the new atom type (which I will be using for CD1 in
the perturbed state) before editing ILE? (actually if I make the atom
type as HC, still the problem persists).

There is a similar question in AMBER archive but I couldn't find how it
was solved.

I would appreciate suggestions.

I have attached the off file (it has HC as the type for perturbed CD1)


Dr. Pradipta Bandyopadhyay
Assistant Professor
Dept. of Biotechnology
Indian Institute of Technology, Guwahati

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Received on Sun Mar 11 2007 - 06:07:04 PDT
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