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

[Somaye Badieyan]

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

...................................................................
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