[gmx-users] change angle type in ffbonded.itp
milad bagheri
milad9bagheri at gmail.com
Tue Nov 1 12:47:36 CET 2016
hello
I'm using Gromacs with
charm27.ff force-field.I adding a new residue (NAG) in force field
I have a problem with water molecules in my system: During
minimization, I have this message:
step X: Water molecule starting at atom XXX can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
My problem is related to protein structure.I changed angletypes part in
ffbonded.itp . so not errors.
my question:
This change how much is true?
-------------- next part --------------
CC NH2 CG321 5 119.6000 494.41 0.0 0.0
H NH2 CG321 5 120.0660 332.42 0.0 0.0
NH2 CG321 HGA2 5 107.6460 445.64 0.0 0.0
NH2 CG321 CG311 5 109.9600 632.32 0.0 0.0
NH2 CG321 OG3C61 5 108.5680 862.36 0.0 0.0
HGA2 CG321 CG311 5 110.5490 383.00 0.0 0.0
HGA2 CG321 OG3C61 5 108.5770 470.32 0.0 0.0
CG311 CG321 OG3C61 5 108.1330 597.39 0.0 0.0
CG321 CG311 HGA1 5 110.5490 383.00 0.0 0.0
CG321 CG311 CG311 5 109.6080 512.48 0.0 0.0
CG321 CG311 NG2S1 5 109.9600 632.32 0.0 0.0
HGA1 CG311 CG311 5 110.5490 383.00 0.0 0.0
HGA1 CG311 NG2S1 5 107.6460 445.64 0.0 0.0
CG311 CG311 NG2S1 5 109.9600 632.32 0.0 0.0
CG311 CG311 HGA1 5 110.5490 383.00 0.0 0.0
CG311 CG311 CG311 5 109.6080 512.48 0.0 0.0
CG311 CG311 OG311 5 108.1330 597.39 0.0 0.0
HGA1 CG311 OG311 5 108.5770 470.32 0.0 0.0
CG311 CG311 CG321 5 109.6080 512.48 0.0 0.0
CG311 CG311 OG3C61 5 108.1330 597.39 0.0 0.0
HGA1 CG311 CG321 5 110.5490 383.00 0.0 0.0
HGA1 CG311 OG3C61 5 108.5770 470.32 0.0 0.0
CG321 CG311 OG3C61 5 108.1330 597.39 0.0 0.0
CG311 CG321 HGA2 5 110.5490 383.00 0.0 0.0
CG311 CG321 OG311 5 108.1330 597.39 0.0 0.0
HGA2 CG321 HGA2 5 108.8360 310.74 0.0 0.0
HGA2 CG321 OG311 5 108.5770 470.32 0.0 0.0
CG331 CG201 NG2S1 5 112.7350 592.57 0.0 0.0
CG331 CG201 OG2D1 5 124.4100 564.87 0.0 0.0
NG2S1 CG201 OG2D1 5 127.1520 546.20 0.0 0.0
CG201 CG331 HGA3 5 108.3850 391.44 0.0 0.0
HGA3 CG331 HGA3 5 108.8360 310.74 0.0 0.0
CG311 NG2S1 CG201 5 119.6000 494.41 0.0 0.0
CG311 NG2S1 HGP1 5 120.0660 332.42 0.0 0.0
CG201 NG2S1 HGP1 5 120.2770 346.27 0.0 0.0
CG311 OG311 HGP1 5 106.5030 477.55 0.0 0.0
CG321 OG3C61 CG311 5 106.9260 720.84 0.0 0.0
CG321 OG311 HGP1 5 106.5030 477.55 0.0 0.0
-------------- next part --------------
CC NH2 CG321 5 119.6000 494.41 119.6000 494.41
H NH2 CG321 5 120.0660 332.42 120.0660 332.42
NH2 CG321 HGA2 5 107.6460 445.64 107.6460 445.64
NH2 CG321 CG311 5 109.9600 632.32 109.9600 632.32
NH2 CG321 OG3C61 5 108.5680 862.36 108.5680 862.36
HGA2 CG321 CG311 5 110.5490 383.00 110.5490 383.00
HGA2 CG321 OG3C61 5 108.5770 470.32 108.5770 470.32
CG311 CG321 OG3C61 5 108.1330 597.39 108.1330 597.39
CG321 CG311 HGA1 5 110.5490 383.00 110.5490 383.00
CG321 CG311 CG311 5 109.6080 512.48 109.6080 512.48
CG321 CG311 NG2S1 5 109.9600 632.32 109.9600 632.32
HGA1 CG311 CG311 5 110.5490 383.00 110.5490 383.00
HGA1 CG311 NG2S1 5 107.6460 445.64 107.6460 445.64
CG311 CG311 NG2S1 5 109.9600 632.32 109.9600 632.32
CG311 CG311 HGA1 5 110.5490 383.00 110.5490 383.00
CG311 CG311 CG311 5 109.6080 512.48 109.6080 512.48
CG311 CG311 OG311 5 108.1330 597.39 108.1330 597.39
HGA1 CG311 OG311 5 108.5770 470.32 108.5770 470.32
CG311 CG311 CG321 5 109.6080 512.48 109.6080 512.48
CG311 CG311 OG3C61 5 108.1330 597.39 108.1330 597.39
HGA1 CG311 CG321 5 110.5490 383.00 110.5490 383.00
HGA1 CG311 OG3C61 5 108.5770 470.32 108.5770 470.32
CG321 CG311 OG3C61 5 108.1330 597.39 108.1330 597.39
CG311 CG321 HGA2 5 110.5490 383.00 110.5490 383.00
CG311 CG321 OG311 5 108.1330 597.39 108.1330 597.39
HGA2 CG321 HGA2 5 108.8360 310.74 108.8360 310.74
HGA2 CG321 OG311 5 108.5770 470.32 108.5770 470.32
CG331 CG201 NG2S1 5 112.7350 592.57 112.7350 592.57
CG331 CG201 OG2D1 5 124.4100 564.87 124.4100 564.87
NG2S1 CG201 OG2D1 5 127.1520 546.20 127.1520 546.20
CG201 CG331 HGA3 5 108.3850 391.44 108.3850 391.44
HGA3 CG331 HGA3 5 108.8360 310.74 108.8360 310.74
CG311 NG2S1 CG201 5 119.6000 494.41 119.6000 494.41
CG311 NG2S1 HGP1 5 120.0660 332.42 120.0660 332.42
CG201 NG2S1 HGP1 5 120.2770 346.27 120.2770 346.27
CG311 OG311 HGP1 5 106.5030 477.55 106.5030 477.55
CG321 OG3C61 CG311 5 106.9260 720.84 106.9260 720.84
CG321 OG311 HGP1 5 106.5030 477.55 106.5030 477.55
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