AMBER Archive (2006)

Subject: Re: AMBER: water prmtop/inpcrd problem

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Oct 06 2006 - 04:17:11 CDT

I dont see any problem here. Your original .pdb file does not have TER
cards in it, while the mod2.pdb has TER cards in it to seperate each
water molecule from each other (which is normal). VMD uses the 'distance'
between 2 atoms to decide whether there is a bond or not (namely its a
guess). If you use these prmtop/inpcrd files in sander, it will not see
this 'virtual' bond that u see in VMD as a bond.

On Thu, 5 Oct 2006, Akshay Patny wrote:

> Dear Amber Users
>
> I am trying to convert a water PDB file into the PRMTOP and
> INPCRD files via LEAP. I am using Amber 8 for the same.
>
> I used ff03 forcefield. In my initial water pdb file
> “water_mod2.pdb”: there are 12 water molecules and I
> have changed the residue names to WAT for leap to recognize
> them as TIP3P water and the atom names are O, H1, and H2 for
> each water molecule. The atom numbers are unique although do
> not start from 1.
>
> I used LEAP to load this water_mod2.pdb file and then saved
> it as PRMTOP (mod2.prmtop) and INPCRD (mod2.inpcrd) as well
> as PDB (mod2.pdb). Now, when I open the PRMTOP/INPCRD files
> using VMD, there is an extra bond between two hydrogens for
> each water molecule. Surprisingly the output PDB file from
> LEAP is perfect when viewed by PDB.
>
> Can anyone guide me why is this happening? I am attaching
> files and the leap output below:
>
> Also LEAP says following .....
> ____________________________________
> (starting new molecule for chain 1)
> (starting new molecule for chain 2)
> (starting new molecule for chain 3)
> ____________________________________
> why it starts a new molecule ... i do not have any chains.
>
> I look forward for suggestions.
>
> Thanks
> Akshay Patny
> _______________________________________________________________________
>
> > try = loadpdb water_mod2.pdb
> Loading PDB file: ./water_mod2.pdb
> (starting new molecule for chain 1)
> (starting new molecule for chain 2)
> (starting new molecule for chain 3)
> total atoms in file: 36
> > saveamberparm try mod2.prmtop mod2.inpcrd
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 0 improper torsions applied
> Building H-Bond parameters.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
>
> res total affected
>
> WAT 12
> )
> (no restraints)
> > savepdb try mod2.pdb
> Writing pdb file: mod2.pdb
> ____________________________________________________________
>
> Akshay Patny
> 

-- 
  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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