AMBER Archive (2006)

Subject: RE: AMBER: water prmtop/inpcrd problem

From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Fri Oct 06 2006 - 09:49:22 CDT

Thanks Dr. Case and DR. Yildirim. I got that.
Akshay Patny

|-----Original Message-----
|From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
|Ilyas Yildirim
|Sent: Friday, October 06, 2006 4:17 AM
|To: amber_at_scripps.edu
|Subject: Re: AMBER: water prmtop/inpcrd problem
|
|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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