[gmx-users] isopeptide bond

Mark Abraham mark.abraham at anu.edu.au
Tue Mar 1 10:47:39 CET 2011



On 03/01/11, zeppelin zeppelin  <zzeppelin87 at gmail.com> wrote:
> 
> Dear GROMACS users,
> 
> 
> 
> I started to work with gromacs (version
> 4.0.5) only several weeks ago and I need your help.
> 
> 
> 

In that case, you'll be best served by starting with the most recent version of GROMACS, not one that's 3 years old. Force field organization has changed, and AMBER forcefields are fully integrated.


> 
>  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: 
> 
> 
> 
> LYN     NZ      1       GLY     C      
> 1       0.13	LYQ     GLQ
> 
> 
> 3. Added new bond type, angle type and
> dihedral type to ffamber99bon.itp:
> 
> 
> 

Why do you think you need to do this? What's wrong with the existing atom and functional types? Use (for example) glutamide and backbone peptides as models for what you want to achieve.


> 
> 
> 
> 
> 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)
> 
> 
> 

But the nitrogen in an isopeptide bond is neutral. N should be fine. Why are you buying trouble?


> 
> 
> 
> 
> 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 bond. 
> 
> 
> 
> 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)? 
> 
> 
> 
> 

It means that there was already an angle type for C-CT-N3 before you invented a new one, and GROMACS is warning you that one definition is replacing the other. It's up to you judge whether that is sensible.

Mark
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