I wanted to post a resolution to this issue for the purposes of the archive.
There are a bunch of similar threads that are just dead-ends, so hopefully
someone finds this useful one day.
The problem described here results from a couple of factors:
1. Incorrect charge assignment for the anomeric carbon (hemiacetal on the
reducing end of the oligosaccharide)
2. A missing exclusion
The proper terminal "patches" for the 45A4/53A6 sugar parameters are found in
Lins and Hunenberger JCC 2005. The authors note instability within this
problematic region due to an overt attraction between O5 (in the ring) and H1
(added as part of the terminal "patch"). The solution is the following:
1. Use the charges provided by Lins and Hunenberger for the reducing end of the
sugar
2. Add an extra exclusion between H1 and O5
A possible workflow for building oligosaccharides derives from a generic polymer
workflow I posted on the Gromacs site
(http://www.gromacs.org/Documentation/How-tos/Polymers), and includes defining a
"start" and "end" residue (non-reducing and reducing ends in the case of
sugars), as well as the monomer repeat unit (which is already defined in the
force field in the case of glucose). Thus, one could apply the following .rtp
entries:
[ GLCN ] ; beta-D-glucose, non-reducing end
[ atoms ]
C4 CH1 0.23200 0
O4 OA -0.64200 0
HO4 H 0.41000 0
C3 CH1 0.23200 1
O3 OA -0.64200 1
HO3 H 0.41000 1
C2 CH1 0.23200 2
O2 OA -0.64200 2
HO2 H 0.41000 2
C6 CH2 0.23200 3
O6 OA -0.64200 3
HO6 H 0.41000 3
C5 CH1 0.37600 4
O5 OA -0.48000 4
C1 CH1 0.232 4
O1 OA -0.360 4
[ bonds ]
C4 C3 gb_26
C4 O4 gb_20
O4 HO4 gb_1
C4 C5 gb_26
C3 O3 gb_20
C3 C2 gb_26
O3 HO3 gb_1
C2 O2 gb_20
C2 C1 gb_26
O2 HO2 gb_1
C6 O6 gb_20
C6 C5 gb_26
O6 HO6 gb_1
C5 O5 gb_20
O5 C1 gb_20
C1 O1 gb_20
O1 +C4 gb_20
[ angles ]
; ai aj ak gromos type
C4 O4 HO4 ga_12
O4 C4 C3 ga_9
O4 C4 C5 ga_9
C3 C4 C5 ga_8
C4 C3 O3 ga_9
C4 C3 C2 ga_8
O3 C3 C2 ga_9
C3 O3 HO3 ga_12
C3 C2 O2 ga_9
C3 C2 C1 ga_8
O2 C2 C1 ga_9
C2 O2 HO2 ga_12
O6 C6 C5 ga_9
C6 O6 HO6 ga_12
C4 C5 C6 ga_8
C4 C5 O5 ga_9
C6 C5 O5 ga_9
C5 O5 C1 ga_10
C2 C1 O5 ga_9
C2 C1 O1 ga_9
O5 C1 O1 ga_9
C1 O1 +C4 ga_10
[ impropers ]
; ai aj ak al gromos type
C4 C6 O5 C5 gi_2
C3 O3 C2 C4 gi_2
C2 O5 O1 C1 gi_2
C5 O4 C3 C4 gi_2
C1 C3 O2 C2 gi_2
[ dihedrals ]
; ai aj ak al gromos type
HO4 O4 C4 C3 gd_30
O4 C4 C3 O3 gd_18
O4 C4 C3 C2 gd_17
C5 C4 C3 O3 gd_17
C5 C4 C3 C2 gd_34
O4 C4 C5 C6 gd_17
C3 C4 C5 C6 gd_34
C3 C4 C5 O5 gd_17
C2 C3 O3 HO3 gd_30
C4 C3 C2 O2 gd_17
C4 C3 C2 C1 gd_34
O3 C3 C2 O2 gd_18
O3 C3 C2 C1 gd_17
C1 C2 O2 HO2 gd_30
C3 C2 C1 O5 gd_17
C3 C2 C1 O1 gd_17
C3 C2 C1 O1 gd_34
O2 C2 C1 O1 gd_18
C5 C6 O6 HO6 gd_30
O6 C6 C5 O5 gd_5
O6 C6 C5 O5 gd_37
C4 C5 O5 C1 gd_29
C5 O5 C1 C2 gd_29
O5 C1 O1 +C4 gd_2
O5 C1 O1 +C4 gd_32
[ GLCR ] ; beta-D-glucose, reducing end
[ atoms ]
C4 CH1 0.23200 0
C3 CH1 0.23200 1
O3 OA -0.64200 1
HO3 H 0.41000 1
C2 CH1 0.23200 2
O2 OA -0.64200 2
HO2 H 0.41000 2
C6 CH2 0.23200 3
O6 OA -0.64200 3
HO6 H 0.41000 3
C5 CH1 0.37600 4
O5 OA -0.48000 4
C1 CH1 0.23200 4
O1 OA -0.53800 4
H1 H 0.41000 4
[ bonds ]
C4 C3 gb_26
C4 C5 gb_26
C3 O3 gb_20
C3 C2 gb_26
O3 HO3 gb_1
C2 O2 gb_20
C2 C1 gb_26
O2 HO2 gb_1
C6 O6 gb_20
C6 C5 gb_26
O6 HO6 gb_1
C5 O5 gb_20
O5 C1 gb_20
C1 O1 gb_20
O1 H1 gb_1
[ angles ]
; ai aj ak gromos type
-C1 -O1 C4 ga_10
-O1 C4 C3 ga_9
-O1 C4 C5 ga_9
C3 C4 C5 ga_8
C4 C3 O3 ga_9
C4 C3 C2 ga_8
O3 C3 C2 ga_9
C3 O3 HO3 ga_12
C3 C2 O2 ga_9
C3 C2 C1 ga_8
O2 C2 C1 ga_9
C2 O2 HO2 ga_12
O6 C6 C5 ga_9
C6 O6 HO6 ga_12
C4 C5 C6 ga_8
C4 C5 O5 ga_9
C6 C5 O5 ga_9
C5 O5 C1 ga_10
C2 C1 O5 ga_9
C2 C1 O1 ga_9
O5 C1 O1 ga_9
C1 O1 H1 ga_12
[ impropers ]
; ai aj ak al gromos type
C4 C6 O5 C5 gi_2
C3 O3 C2 C4 gi_2
C2 O5 O1 C1 gi_2
C5 O4 C3 C4 gi_2
C1 C3 O2 C2 gi_2
[ dihedrals ]
; ai aj ak al gromos type
-C1 -O1 C4 C3 gd_30
-O1 C4 C3 O3 gd_18
-O1 C4 C3 C2 gd_17
C5 C4 C3 O3 gd_17
C5 C4 C3 C2 gd_34
-O1 C4 C5 C6 gd_17
C3 C4 C5 C6 gd_34
C3 C4 C5 O5 gd_17
C2 C3 O3 HO3 gd_30
C4 C3 C2 O2 gd_17
C4 C3 C2 C1 gd_34
O3 C3 C2 O2 gd_18
O3 C3 C2 C1 gd_17
C1 C2 O2 HO2 gd_30
C3 C2 C1 O5 gd_17
C3 C2 C1 O1 gd_17
C3 C2 C1 O1 gd_34
O2 C2 C1 O1 gd_18
C5 C6 O6 HO6 gd_30
O6 C6 C5 O5 gd_5
O6 C6 C5 O5 gd_37
C4 C5 O5 C1 gd_29
C5 O5 C1 C2 gd_29
O5 C1 O1 H1 gd_2
O5 C1 O1 H1 gd_32
[ exclusions ]
H1 O5
Hopefully this information is useful.
-Justin
Somaye Badieyan wrote:
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/*
/.................................................................../
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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