[gmx-users] isopeptide bond

zeppelin zeppelin zzeppelin87 at gmail.com
Tue Mar 1 09:43:56 CET 2011

Dear GROMACS users,

I started to work with gromacs (version 4.0.5) only several weeks ago and I
need your help. Now I am trying to add a new *isopeptide bone* to connect
Lys and Gly (to make a dimer of *ubiquitin*). I use AMBER force field.

What I did:

1. Added new type of residues to ffamber.rtp

LIQ – LYN that is close enough to GLY (GLQ) to make an isopeptide bond.
Distance – 0.13

2. I added this line to specbond.dat:


3. Added new bond type, angle type and dihedral type to ffamber99bon.itp:

For example:

[ angletypes ]

; i j k func           th0    *cth*

HW OW HW 1 104.520 836.800 ; TIP3P water

HW HW OW 1 127.740 0.000 ; (found in crystallographic water with 3 bonds)

C C O 1 120.000 669.440 ; new99


new lines:

C CT N3 1 110.100 527.184 ; FOR UBIQ YULIAN            line 344

C N3 H 1 120.000 418.400 ; FOR UBIQ YULIAN

N3 C O 1 122.900 669.440 ; FOR UBIQ YULIAN

CT C N3 1 116.600 585.760 ; FOR UBIQ YULIAN

C N3 CT 1 121.900 418.400 ; FOR UBIQ YULIAN

C N3 H 1 120.000 418.400 ; FOR UBIQ YULIAN

 Here I added a new angle types just by copying a close type of angle in
simple peptide bone and changing N to N3 (for isopeptide bone)

4. But in ffamber99.atp one can found that these atoms are different (sp2
and sp3 type of hybridization):

amber99_34 14.01000 ; N sp2 nitrogen in amide groups

amber99_39 14.01000 ; N3 sp3 N for charged amino groups (Lys, etc)

5. I checked in PyMol the real value of different angles in isopeptide bond
and found, of course, that they are differ from angles in simple peptide

6. So when I change N to N3 I did not get a real isippeptide bone. And
my *question
*is: How to make a new isopeptide bone with correct value of angles and
dihedrals. I can simply change the value of angle (by measuring in pymol),
but I do not know what is *cth * in [ angletypes ] section of
ffamber99bon.itp and how to change it correctly.

P. S. After this change I have such a warning in gromacs runnings

"WARNING 1 [file ffamber99bon.itp, line 344]:

Overriding Angle parameters.

old: 111.2 669.44 111.2 669.44

new: C CT N3 1 110.100 527.184"

What does it really mean (during editing ffamber99bon.itp I just added
several lines and did not remove anything)?


Yulian Gavrilov
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