[gmx-users] Carbohydrate simulation: problem with the terminal atoms

[nishap.patel at utoronto.ca]

I am not sure if you have looked through this paper, but it gives the  
parameters for sugars.

A new GROMOS force field for hexopyranose-based carbohydrates by RD Lins, 2005

A biomolecular force field based on the free enthalpy of hydration and  
solvation: The GROMOS force?field parameter sets 53A5 and 53A6- C  
Oostenbrink, 2004

Hope that helps.

Nisha P



Quoting Somaye Badieyan <badieyan at yahoo.com>:

> Hi everyone,
>
>
>
> I am using g53a6 force filed for the simulation of cellulose.   
> However it seems
> that parametrization works only for the sugar blocked linked together and no
> terminal atoms for terminal residues are defined there (I mean the start and
> end atom, H and O atom at the beginning linked to c4 and H atom at the last
> Sugar residue linked to O1). I tried to solve the problem by making the
> topology file removing the start OH and end H group from the initial  
>  PDB file to 
> have the topology file made by g53a6 and later add the parameters of OH and H
> to the topology file. The problem is at the time of minimization almost no
> change in energy (not converged even after 7325 step) with the maximum force
> (about 9e+03) on the H of new added OH group (the start OH group). and when I
> checked the output of minimization step I found the HO position and   
> C2 and C3,
> O3 atoms are deformed and the defined angles/bonds/dihedral of this   
> new OH are
> not kept (the other H group the the other side, end, is fine). I know the
> problem is due to the way I defined the parameters but I do not know what the
> problem exactly is. Since the original topology file without the   
> terminal atoms
> start from 1, the terminal atoms are added at the end of gro file   
> and topology
> file (although OH group is part of first residue):
>
>
>
> the molecule is a cellotetetraose and here is the added part to top   
> file (Atom
> number: H at end: 57 ,  O at start:58,   H at start:59):
>
>
>
> ; residue 1001 GLCB rtp GLCB q 
> 0.0
>
>      1       
> CH1   1001   GLCB    
> C4      1     
> 0.332     13.019   ; qtot 0.232
>
>      2       
> CH1   1001   GLCB    
> C3      2     
> 0.232     13.019   ; qtot 0.464
>
>      3        
> OA   1001   GLCB    
> O3      2    
> -0.642    15.9994   ; qtot -0.178
>
>     
> 4          H  
> 1001   GLCB    HO3     
> 2       0.41     
> 1.008   ; qtot 0.232
>
>         .
>
>         .
>
>         .
>
>    
> 56         OA  
> 1004   GLCB     O1    
> 20     -0.642    15.9994   ; qtot
> -0.20
>
>     57         
> H   1004   GLCB   
> HO1     20     
> 0.282      1.008   ; qtot 0
>
> ;added later to 1000 GLCB
>
>     58        
> OA   1001   GLCB    
> O4      1    
> -0.542    15.9994   ;
>
>     59         
> H   1001   GLCB   
> HO4      1     
> 0.442      1.008   ;
>
>
>
> [ bonds ]
>
> ;  ai    aj
> funct           
> c0           
> c1            c2           
> c3
>
>     1     2    
> 2    gb_26
>
>     1    11    
> 2    gb_26
>
> .
>
> .
>
> .
>
>   55    56     2   
> gb_20
>
>    56    57    
> 2    gb_1
>
>    58     1    
> 2    gb_20
>
>    58    59    
> 2    gb_1
>
>
>
> [ angles ]
>
> ;  ai    aj    ak
> funct           
> c0           
> c1           
> c2            c3
>
>     2     1   
> 11     2    ga_8
>
>     1     2    
> 3     2    ga_9
>
>     1     2    
> 5     2    ga_8
>
> .
>
> .
>
> .
>
>    55    56   
> 57     2    ga_12
>
>    11     1   
> 58     2    ga_9
>
>    58     1    
> 2     2    ga_9
>
>     1    58   
> 59     2    ga_12
>
>
>
> [ dihedrals ]
>
> ;  ai    aj    ak    al
> funct           
> c0           
> c1           
> c2           
> c3           
> c4            c5
>
>    11     1    
> 2     3     1    gd_17
>
>    11     1    
> 2     5     1    gd_34
>
>     2     1   
> 11     8     1    gd_34
>
> .
>
> .
>
> .
>
>    59    58    
> 1     2     1    gd_30
>
>    58     1    
> 2     3     1    gd_18
>
>    58     1    
> 2     5     1    gd_17
>
>    58     1    
> 11    8     1    gd_17
>
>
>
> [ dihedrals ]
>
> ;  ai    aj    ak    al
> funct           
> c0           
> c1           
> c2            c3
>
> .
>
> .
>
> .
>
>    11     2   
> 58     1     2    gi_2
>
>
>
>
>
> I prepare this parameters based on the other OH group in the sugars and
> parameters of link oxygen (the shared oxygen at the position of   
> glycosidic bond
> that is expected to be O4 group of the next residue).
>
>  
>
> I
> did not use the PRODRG since i need 53a6 and I found for   
> carbohydrate there is
> too much different between the parameters in 53a6 and 43a1. Somewhere it ahs
> been mentioned to change the terminal database file (.tdb), however   
> I think it
> may make the problem more complicated.
>
>
>
> Your help is appreciated.
>
> -Somaye
>
>  
>
> ...................................................................
>
> Somayesadat Badieyan
>
> PhD Candidate and Research Assistant
>
> Biological Syatems Engineering
>
> 201 Seitz Hall, Virginia Tech
>
> Blacksburg,
> VA 24060
>
> ...................................................................