[gmx-users] adding new residue
fatemeh ramezani
fr_750 at yahoo.com
Sun Jan 18 19:26:36 CET 2015
Dear gmx-usersI want to simulate collagen molecule by gromacs. I produce hydroxyprolin parameter by swissparam site:
; ----
; Built itp for zinc_901791.mol2
; by user vzoete Mon Jan 12 11:37:34 CET 2015
; ----
;
[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
CR 6 12.0110 0.0 A 0.387541 0.230120
HCMM 1 1.0079 0.0 A 0.235197 0.092048
CO2M 6 12.0110 0.0 A 0.356359 0.292880
O2CM 8 15.9994 0.0 A 0.302905 0.502080
OR 8 15.9994 0.0 A 0.315378 0.636386
HOR 1 1.0079 0.0 A 0.040001 0.192464
NRP 7 14.0067 0.0 A 0.329632 0.836800
HNRP 1 1.0079 0.0 A 0.040001 0.192464
[ pairtypes ]
; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS
CR CR 1 0.338541 0.041840
CR HCMM 1 0.286869 0.062059
CR CO2M 1 0.347450 0.110698
CR O2CM 1 0.320723 0.144938
CR OR 1 0.326960 0.163176
CR HOR 1 0.189271 0.089737
CR NRP 1 0.334087 0.187114
CR HNRP 1 0.189271 0.089737
[ moleculetype ]
; Name nrexcl
zinc_901791 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CR 1 LIG C1 1 0.0000 12.0110
2 CR 1 LIG C2 2 0.2800 12.0110
3 HCMM 1 LIG H1 3 0.0000 1.0079
4 CR 1 LIG C3 4 0.5030 12.0110
5 CR 1 LIG C4 5 0.3970 12.0110
6 HCMM 1 LIG H2 6 0.0000 1.0079
7 CO2M 1 LIG C5 7 0.9060 12.0110
8 O2CM 1 LIG O1 8 -0.9000 15.9994
9 OR 1 LIG O2 9 -0.6800 15.9994
10 HCMM 1 LIG H3 10 0.0000 1.0079
11 HCMM 1 LIG H4 11 0.0000 1.0079
12 HCMM 1 LIG H5 12 0.0000 1.0079
13 HCMM 1 LIG H6 13 0.0000 1.0079
14 HOR 1 LIG H7 14 0.4000 1.0079
15 NRP 1 LIG N1 15 -0.9060 14.0067
16 HNRP 1 LIG H8 16 0.4500 1.0079
17 HNRP 1 LIG H9 17 0.4500 1.0079
18 O2CM 1 LIG O3 18 -0.9000 15.9994
[ bonds ]
; ai aj fu b0 kb, b0 kb
7 8 1 0.12610 587519.8 0.12610 587519.8
7 18 1 0.12610 587519.8 0.12610 587519.8
1 5 1 0.15080 256422.3 0.15080 256422.3
1 2 1 0.15080 256422.3 0.15080 256422.3
1 10 1 0.10930 287014.9 0.10930 287014.9
1 11 1 0.10930 287014.9 0.10930 287014.9
2 3 1 0.10930 287014.9 0.10930 287014.9
2 4 1 0.15080 256422.3 0.15080 256422.3
2 9 1 0.14180 303937.5 0.14180 303937.5
4 12 1 0.10930 287014.9 0.10930 287014.9
4 13 1 0.10930 287014.9 0.10930 287014.9
4 15 1 0.14800 231490.7 0.14800 231490.7
5 6 1 0.10930 287014.9 0.10930 287014.9
5 7 1 0.15100 230648.0 0.15100 230648.0
5 15 1 0.14800 231490.7 0.14800 231490.7
9 14 1 0.09720 469365.3 0.09720 469365.3
15 16 1 0.10280 371144.2 0.10280 371144.2
15 17 1 0.10280 371144.2 0.10280 371144.2
[ pairs ]
; ai aj fu
1 12 1
1 13 1
1 14 1
1 8 1
1 18 1
1 16 1
1 17 1
2 6 1
2 7 1
2 16 1
2 17 1
3 5 1
3 10 1
3 11 1
3 12 1
3 13 1
3 15 1
3 14 1
4 10 1
4 11 1
4 14 1
4 6 1
4 7 1
5 9 1
5 12 1
5 13 1
6 10 1
6 11 1
6 8 1
6 18 1
6 16 1
6 17 1
7 10 1
7 11 1
7 16 1
7 17 1
8 15 1
9 10 1
9 11 1
9 12 1
9 13 1
9 15 1
10 15 1
11 15 1
12 16 1
12 17 1
13 16 1
13 17 1
15 18 1
[ angles ]
; ai aj ak fu th0 kth ub0 kub th0
2 1 5 1 109.6080 512.48
2 1 10 1 110.5490 383.00
2 1 11 1 110.5490 383.00
5 1 10 1 110.5490 383.00
5 1 11 1 110.5490 383.00
10 1 11 1 108.8360 310.74
1 2 3 1 110.5490 383.00
1 2 4 1 109.6080 512.48
1 2 9 1 108.1330 597.39
3 2 4 1 110.5490 383.00
3 2 9 1 108.5770 470.32
4 2 9 1 108.1330 597.39
2 4 12 1 110.5490 383.00
2 4 13 1 110.5490 383.00
2 4 15 1 106.4930 710.01
12 4 13 1 108.8360 310.74
12 4 15 1 106.2240 525.13
13 4 15 1 106.2240 525.13
1 5 6 1 110.5490 383.00
1 5 7 1 98.4220 198.73
1 5 15 1 106.4930 710.01
6 5 7 1 108.9040 316.16
6 5 15 1 106.2240 525.13
7 5 15 1 112.2380 631.11
5 7 8 1 114.6890 728.07
5 7 18 1 114.6890 728.07
8 7 18 1 130.6000 711.20
2 9 14 1 106.5030 477.55
4 15 5 1 112.2510 519.10
4 15 16 1 111.2060 346.87
4 15 17 1 111.2060 346.87
5 15 16 1 111.2060 346.87
5 15 17 1 111.2060 346.87
16 15 17 1 107.7870 348.08
[ dihedrals ]
; ai aj ak al fu phi0 kphi mult phi0
1 2 4 12 9 0.00 1.3389 1
1 2 4 12 9 180.00 -1.3180 2
1 2 4 12 9 0.00 0.5523 3
1 2 4 13 9 0.00 1.3389 1
1 2 4 13 9 180.00 -1.3180 2
1 2 4 13 9 0.00 0.5523 3
1 2 4 15 9 0.00 -1.3556 1
1 2 4 15 9 180.00 1.1506 2
1 2 4 15 9 0.00 1.2343 3
1 2 9 14 9 180.00 0.5648 2
1 2 9 14 9 0.00 0.4937 3
1 5 7 8 9 180.00 2.6401 2
1 5 7 18 9 180.00 2.6401 2
1 5 15 4 9 0.00 0.5230 3
1 5 15 16 9 0.00 0.3891 3
1 5 15 17 9 0.00 0.3891 3
2 1 5 6 9 0.00 1.3389 1
2 1 5 6 9 180.00 -1.3180 2
2 1 5 6 9 0.00 0.5523 3
2 1 5 7 9 0.00 0.6276 3
2 1 5 15 9 0.00 -1.3556 1
2 1 5 15 9 180.00 1.1506 2
2 1 5 15 9 0.00 1.2343 3
2 4 15 5 9 0.00 0.5230 3
2 4 15 16 9 0.00 0.3891 3
2 4 15 17 9 0.00 0.3891 3
3 2 1 5 9 0.00 1.3389 1
3 2 1 5 9 180.00 -1.3180 2
3 2 1 5 9 0.00 0.5523 3
3 2 1 10 9 0.00 0.5941 1
3 2 1 10 9 180.00 -2.8995 2
3 2 1 10 9 0.00 0.6569 3
3 2 1 11 9 0.00 0.5941 1
3 2 1 11 9 180.00 -2.8995 2
3 2 1 11 9 0.00 0.6569 3
3 2 4 12 9 0.00 0.5941 1
3 2 4 12 9 180.00 -2.8995 2
3 2 4 12 9 0.00 0.6569 3
3 2 4 13 9 0.00 0.5941 1
3 2 4 13 9 180.00 -2.8995 2
3 2 4 13 9 0.00 0.6569 3
3 2 4 15 9 0.00 1.4477 1
3 2 4 15 9 180.00 -1.1088 2
3 2 4 15 9 0.00 0.5816 3
3 2 9 14 9 0.00 1.2468 1
3 2 9 14 9 180.00 -0.5774 2
3 2 9 14 9 0.00 0.7238 3
4 2 1 5 9 0.00 0.2134 1
4 2 1 5 9 180.00 1.4267 2
4 2 1 5 9 0.00 0.6945 3
4 2 1 10 9 0.00 1.3389 1
4 2 1 10 9 180.00 -1.3180 2
4 2 1 10 9 0.00 0.5523 3
4 2 1 11 9 0.00 1.3389 1
4 2 1 11 9 180.00 -1.3180 2
4 2 1 11 9 0.00 0.5523 3
4 2 9 14 9 180.00 0.5648 2
4 2 9 14 9 0.00 0.4937 3
4 15 5 6 9 0.00 0.5146 3
4 15 5 7 9 0.00 0.5230 3
5 1 2 9 9 0.00 -1.4393 1
5 1 2 9 9 180.00 3.6777 2
5 1 2 9 9 0.00 0.9958 3
5 15 4 12 9 0.00 0.5146 3
5 15 4 13 9 0.00 0.5146 3
6 5 1 10 9 0.00 0.5941 1
6 5 1 10 9 180.00 -2.8995 2
6 5 1 10 9 0.00 0.6569 3
6 5 1 11 9 0.00 0.5941 1
6 5 1 11 9 180.00 -2.8995 2
6 5 1 11 9 0.00 0.6569 3
6 5 7 8 9 0.00 -0.2218 3
6 5 7 18 9 0.00 -0.2218 3
6 5 15 16 9 0.00 0.5439 3
6 5 15 17 9 0.00 0.5439 3
7 5 1 10 9 0.00 -0.2929 3
7 5 1 11 9 0.00 -0.2929 3
7 5 15 16 9 0.00 0.5230 3
7 5 15 17 9 0.00 0.5230 3
8 7 5 15 9 180.00 1.2552 2
9 2 1 10 9 0.00 -1.3682 1
9 2 1 10 9 180.00 2.2426 2
9 2 1 10 9 0.00 0.5858 3
9 2 1 11 9 0.00 -1.3682 1
9 2 1 11 9 180.00 2.2426 2
9 2 1 11 9 0.00 0.5858 3
9 2 4 12 9 0.00 -1.3682 1
9 2 4 12 9 180.00 2.2426 2
9 2 4 12 9 0.00 0.5858 3
9 2 4 13 9 0.00 -1.3682 1
9 2 4 13 9 180.00 2.2426 2
9 2 4 13 9 0.00 0.5858 3
9 2 4 15 9 0.00 0.6276 3
10 1 5 15 9 0.00 1.4477 1
10 1 5 15 9 180.00 -1.1088 2
10 1 5 15 9 0.00 0.5816 3
11 1 5 15 9 0.00 1.4477 1
11 1 5 15 9 180.00 -1.1088 2
11 1 5 15 9 0.00 0.5816 3
12 4 15 16 9 0.00 0.5439 3
12 4 15 17 9 0.00 0.5439 3
13 4 15 16 9 0.00 0.5439 3
13 4 15 17 9 0.00 0.5439 3
15 5 7 18 9 180.00 1.2552 2
[ dihedrals ]
; ai aj ak al fu xi0 kxi xi0 kxi
1 2 5 10 2 0.00 0.0000
1 2 5 11 2 0.00 0.0000
2 4 1 9 2 0.00 0.0000
2 4 1 3 2 0.00 0.0000
5 7 1 15 2 0.00 0.0000
5 7 1 6 2 0.00 0.0000
7 8 5 18 2 0.00 107.1941
4 15 2 12 2 0.00 0.0000
4 12 2 13 2 0.00 0.0000
15 4 5 16 2 0.00 0.0000
15 4 5 17 2 0.00 0.0000
#ifdef POSRES_LIGAND
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
2 1 1000 1000 1000
4 1 1000 1000 1000
5 1 1000 1000 1000
7 1 1000 1000 1000
8 1 1000 1000 1000
9 1 1000 1000 1000
15 1 1000 1000 1000
18 1 1000 1000 1000
#endif
I added atomtypes section in .atp file. I added hydroxyprolin hydrogen data in hdb file.
I dded [bonds], [angles], [dihedrals] and 2th [dihedrals] in ffbonded.itp file respectively in [ bondtypes ], [ anglestypes ], [dihedraltypes ] and 2th [dihedraltypes ].in the first grompp, this error appeared:number of coordinates in coordinate file (x.pdb, 72323)
does not match topology (x.top, 95870)
that the difference is equal to sol atom number that is 23547I dont know how can I solve this problem. I appreciate any help.
Fatemeh Ramezani
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