AMBER Archive (2002)

Subject: several questions

From: David Keller (dkeller_at_unm.edu)
Date: Tue Jul 23 2002 - 17:24:04 CDT

Three problems:
1. We are trying to learn how to run Amber simulations (using Amber 7).
 Our molecule is a polymerase with a bound NTP. In the pdb file, we
modified the residue name for the NTP to "DTN", but we see that the
prototype for DTN contains no phosphate groups. When leap reads in the
pdb file it adds the phosphorus and oxygens of the phosphate groups, but
we see that these atoms have no charges, bonds, or other appropriate
attributes.
    Is there a pre-defined residue type for FULL nucleotides, including
the tri-phosphate?
    Is there a pre-defined triphospate defined as a residue in its own
right?
    Is there some standard way to deal with this problem?

2. Our molecule also has magnesium ions bound to it. Is there a
predefined set of parameters (or residue, or atom, or unit) for
magnesium ions?

3. After running the tutorial on polyAT we tried to animate it using
VMD, but VMD would not read the prmtop and inpcrd files. It gave us a
message "Not equipped to read perturbation parm file". Is this a known
problem? Have formats changed recently?
Thanks,
David Keller