AMBER Archive (2005)

Subject: AMBER: loading pdb in leap to create parmeter files

From: mrbroad_at_ilstu.edu
Date: Sat Feb 05 2005 - 15:24:04 CST

Dear AMBER:

I am currently running AMBER 8. I downloaded a pdb from the protein databank
website. I loaded the pbd file into leap in hopes of creating .prmtop and
.inpcrd files to run a minimization and molecular dynamics run. However; when
trying to create these files I recieve an error message in the univeral editor
stating that a number of atoms ( all atoms involved in heteroatoms specifically
Guanosine triphosphate (GTP) and manganese ) stating, "FATAL: Atom .R,GTO
615>.A<pg 1> does not have a type." This is just one line of the error
message,
but same applies to all atoms in the GTP molecule and Mn.

>From here I selected the atoms without a type and filled in manually the atom
types. Then when I tried to create my .prmtop and .inpcrd file I got new
errors.
I.E.
     1. "Could not find bond parameter for : P-CT"
     2. "Could not find angle Parameter: P-CT-P
     3. "** No torsion terms for P-CT-P-O2"

Again my parameter files were not built. I saw with some of the mails that you
have recieved before, and with some of the FAQ's that I might need to use the
leap command, "addPdbAtomMap." I tried some different attemps at the this
command, but I keep getting a message saying that the lists that I input are
not
lists, which means I don't know how to use this command.

So my first question is, is addpdbatommap the correct command that I need to
use, and if so how do I use it?

If not what do I need to do to get parmeter files built for my pdb including
the
heteroatoms?

The pdb that I am using off of the databank is ID: 1KHB . From this pdb file I
removed to waters for simplicity at the time.

Any Help is greatly Appreciated.

Matthew

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