AMBER Archive (2006)

Subject: RE: AMBER: A dummy atom on the center of solute molecule

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Sun May 28 2006 - 23:26:33 CDT

Dear Acci.

> Firstly, I want to put the dummy atom on the middle point of the double
> bond(C=C). But,I couldn't put the dummy atom on the correct middle point of
> the double bond because xleap graphics is three dimensions using
> mouse(i.e.I can put the atom correctly on x-y plane, but I can't put
> correctly along z-axis ) How can I put
> the dummy atom on correct middle point of the double bond ?

The question is NOT to put the dummy atom in an EXACT location. What do u
need to do with this dummy atom? If u dont connect that dummy atom to some
atoms, in the MD simulation, it is going to fly away from that position.
So, if u connect that dummy atom with some atoms, and define the bond
lengths of those bonds in the .frcmod file, in the minimization process,
it's going to come to the right position.

> Secondly, I executed antechamber program to make prep file of ligand
> molecule as following,
>
> antechamber -i BUT.pdb -fi pdb -o BUT.prep -fo prepi
>
> And, I send you BUT.pdb file and BUT.prep file
>
> I doubt the following line form in prep file ,
>
> 16 X 1 0 1 3.247 180.000 nan 0.00000
>
> Do you think this line is right ?

No, this is not right. It should have the dummy atom name in it (but I
dont see it).

PS: Send your emails to the AMBER mailing list. Someone else might help u,
too. 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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