AMBER Archive (2008)

Subject: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER?

From: Edyta Malolepsza (
Date: Thu Mar 06 2008 - 06:23:06 CST

Dear Amber users,

Some chemically equivalent atoms (oxygen atoms in COO- for ASP and GLU
and for all terminal COO- or hydrogen atoms in NH2 for ASN and GLN)
seem to be not equivalent in AMBER9.

Simple example: let dipeptide {NASP CVAL} built by LEaP be a reference
structure R; R with swapped positions of oxygens in COO- in aspartate
be a test structure 1T; R with swapped oxygens in COO- in C terminus
be a test structure 2T. All structures should have the same energy and
gradient both in minimization process and MD (independent of method
and conditions), but they are not the same. T structures can come from
'raw' structure R built by LEaP or from R minimized by SANDER -
independently of method still I found differences in energies and
gradients between R and T's.

The reason can be in order of atoms in IMPROPER angles for NH2 and COO- groups.

According to atom order is as
follows: "the central atom is the third atom in the improper
    and the order of the other three is determined alphabetically by
atom type and if types are the same by atom number". In case of
IMPROPER for COO- group it means CT-O2-C-O2. This one which gives the
same results for swapped atoms is O2-CT-C-O2.

After including frcmod file with new order of atoms for IMPROPER it
was always applied to prmtop file only for first COO- group in the
system. The others IMPROPER angles had original order of atoms and
these oxygen atoms still were treated not equivalently.

Except of question why atom order from my frcmod file was applied only
for the first COO- group in a system, I have more important question:
how to force proper order of atoms for IMPROPER angles? It is possible
without changing source code for LEaP?

Energy difference coming from atom swap described above is relatively
small, but in my work it is important and I will appreciate all

With best regards,

Edyta Malolepsza
source leaprc.ff03
loadamberparams frcmod.perm
peptide = sequence {NASP CVAL}
saveamberparm peptide test.prmtop test.inpcrd

new term for improper in COO- group




O2-CT-C -O2 1.2 180.0 2.0 Using original
values - it's only test


example of mdin.min
   imin=1, maxcyc=50, ncyc=1,
   cut=300.0, igb=2, saltcon=0.2,
   ntpr=1, ntx=1, ntb=0
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