AMBER Archive (2006)

Subject: AMBER: erroneous placement of TER card

From: Gregory Sandala (sandala_at_rsc.anu.edu.au)
Date: Thu Nov 16 2006 - 03:12:43 CST

Dear Amber users,

My name is Greg and I'm a fairly new user of Amber (by the way, great
program!).
I've encountered a strange phenomenon that I hope you can help me
with. The
system has 107170 atoms in 30090 residues (including 28699 waters).
Using Leap
I've added a bond between two specific atoms (in different residues),
solvated
the system (with both solvateoct and solvatebox separately, see
below) and
added Na+ counter ions.

Ultimately, the problem boils down to the following error when I
attempt to run
PMEMD for an MD simulation beginning from a restart file obtained from a
successful SANDER run using the same topology.

   3. ATOMIC COORDINATES AND VELOCITIES
------------------------------------------------------------------------
--------

begin time read from input coords = 25.000 ps

| ERROR: Bad residue/molecule data in prmtop!
| Residue 739(atoms 11384- 11398) is in multiple
molecules.

Again, the exact same run executes successfully if I use the SANDER
executable instead
of PMEMD.

When I inspect a PDB file of this structure made with the AMBPDB
utility I
notice a 'TER' card has automatically been inserted in the middle of
a residue
(between atoms 11388 and 11389). This residue is not involved in the
bond that
I manually inserted. Interestingly, when I use 'savepdb' directly
through LEAP,
this 'TER' is not present in the resulting PDB (nor was it present in
the
protein PDB that I loaded into leap).

At first I thought it had something to do with the size of the system
(some form
of a numerical loop that clashed). To test this I tried smaller
buffers and
various closenesses in the solvation card, as well as trying
solvateoct and
solvatebox. However, I would always get the TER card present in the
resulting
PDB from ambpdb and PMEMD would not like the topology. Strangely, if
I re-run
LEAP without the BOND command only (i.e., retaining the solvation and
addions
commands), then PMEMD initializes just fine and the PDB files
generated using
AMBPDB do not contain the previously mentioned TER.

This all seems quite strange to me and I'm wondering if any of you
can provide
me with some insights into this problem.

With best wishes,
Greg 

---
Gregory M. Sandala
School of Chemistry
University of Sydney
Sydney NSW 2006
Australia
Ph:  +61 2 9351 5361
sandala_at_chem.usyd.edu.au

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