AMBER: amber 8 leap topology file dihedral term problem

From: Angela Liu <>
Date: Tue, 28 Jun 2005 06:59:57 -0700 (PDT)

Dear Amber users,

Following the DNA 10-mer polyAT tutorial, I use tleap
to create the topoloty files for the DNA in vacuum and
in water. If I create a copy of the model before I do
the first "saveamberparm" to create the vacuum
topology, and then solvate the copy to create the
solvated topology, I get the same .prmtop file as the
website. However, if I do not copy the model, but
save two topology files (vacuum and solvated) on the
same model, the final solvated topology file has a
different number of dihedral terms (NPHIH). If I use
rdparm to list all the dihedral terms in these two
files, the atoms involved are also different.
Furthermore, when I use these two different topology
files but the same .inpcrd file to do a single-point
energy evaluation, I found a DIHED difference of about
10 kcal/mol between these two topology files.

A similar problem is that if I try to load a PDB file
from an MD trajectory into leap and then do
"saveamberparm", I would create a new topology file
that is different in NPHIH from the original topology
file used in the MD simulation.

I am using Amber 8, FF03 on Red Hat Enterprise Linux
with all bug fixes installed. I am attaching the
script file I used in tleap, and the differences I
found from the above comparisons here.
> model = loadpdb "xxx.pdb"
> savepdb model xxx_leap.pdb
> model2 = copy model
> saveamberparm model model_vac.prmtop
> model_vac.inpcrd
> addions model Na+ 0
> solvateoct model TIP3PBOX 8.0
> savepdb model model_wat.pdb
> saveamberparm model model_wat.prmtop
> model_wat.inpcrd
> addions model2 Na+ 0
> solvateoct model2 TIP3PBOX 8.0
> savepdb model2 model2_wat.pdb
> saveamberparm model2 model2_wat.prmtop
> model2_wat.inpcrd

The two .inpcrd files are identical. But a "diff" of
model_wat.prmtop and model2_wat.prmtop results in the
following differences (I am only including the first
difference, there are a lot more differences):

> model_wat.prmtop
> 7c7
> > 9560 17 9138 452 554 694
> 1056 1238 0
> 0
> ---
> model2_wat.prmtop
> < 9560 17 9138 452 554 694
> 1077 1238 0
> 0

In the DNA tutorial webpage, the solvated .prmtop file
has 1077 NPHIH as well.

The single-point energy calculation on
> model_wat.prmtop and model_wat.inpcrd:
> " DIHED = 467.8807".
> model2_wat.prmtop and model2_wat.inpcrd:
> " DIHED = 456.0253", which is about 10
kcal/mol lower in
> energy.

Please let me know if this is indeed a bug, or
something I didn't do right.

Thank you so much for your time and help!

Best wishes,

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Received on Tue Jun 28 2005 - 15:53:00 PDT
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