[gmx-users] change atom type in ffbonded.itp

Mostafa Khedrinia mostafakhedrinia at gmail.com
Tue Nov 1 13:10:36 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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