Editconf

1 描述

editconf 有以下作用：

• 将.gro 文件重新转换为.pdb 文件。
• 建立盒子，并设置盒子参数。

editconf converts generic structure format to .gro, .g96 or .pdb.

The box can be modified with options -box, -d and -angles. Both -box and -d will center the system in the box.

Option -bt determines the box type: triclinic is a triclinic box, cubic is a rectangular box with all sides equal dodecahedron represents a rhombic dodecahedron and octahedron is a truncated octahedron. The last two are special cases of a triclinic box. The length of the three box vectors of the truncated octahedron is the shortest distance between two opposite hexagons. The volume of a dodecahedron is 0.71 and that of a truncated octahedron is 0.77 of that of a cubic box with the same periodic image distance.

Option -box requires only one value for a cubic box, dodecahedron and a truncated octahedron.

With -d and a triclinic box the size of the system in the x, y and z directions is used. With -d and cubic, dodecahedron or octahedron boxes, the dimensions are set to the diameter of the system (largest distance between atoms) plus twice the specified distance.

Option -angles is only meaningful with option -box and a triclinic box and can not be used with option -d.

When -n or -ndef is set, a group can be selected for calculating the size and the geometric center, otherwise the whole system is used.

-rotate rotates the coordinates and velocities.

-princ aligns the principal axes of the system along the coordinate axes, this may allow you to decrease the box volume, but beware that molecules can rotate significantly in a nanosecond.

Scaling is applied before any of the other operations are performed. Boxes can be scaled to give a certain density (option -density). A special feature of the scaling option, when the factor -1 is given in one dimension, one obtains a mirror image, mirrored in one of the plains, when one uses -1 in three dimensions a point-mirror image is obtained.

Groups are selected after all operations have been applied.

Periodicity can be removed in a crude manner. It is important that the box sizes at the bottom of your input file are correct when the periodicity is to be removed.

When writing .pdb files, B-factors can be added with the -bf option. B-factors are read from a file with with following format: first line states number of entries in the file, next lines state an index followed by a B-factor. The B-factors will be attached per residue unless an index is larger than the number of residues or unless the -atom option is set. Obviously, any type of numeric data can be added instead of B-factors. -legend will produce a row of CA atoms with B-factors ranging from the minimum to the maximum value found, effectively making a legend for viewing.

With the option -mead a special pdb (pqr) file for the MEAD electrostatics program (Poisson-Boltzmann solver) can be made. A further prerequisite is that the input file is a run input file. The B-factor field is then filled with the Van der Waals radius of the atoms while the occupancy field will hold the charge.

The option -grasp is similar, but it puts the charges in the B-factor and the radius in the occupancy.

Finally with option -label editconf can add a chain identifier to a pdb file, which can be useful for analysis with e.g. rasmol.

To convert a truncated octrahedron file produced by a package which uses a cubic box with the corners cut off (such as Gromos) use: editconf -f <in> -rotate 0 45 35.264 -bt o -box <veclen> -o <out> where veclen is the size of the cubic box times sqrt(3)/2.

2 文件

option	filename	type	description
-f	conf.gro	Input	Structure file: gro g96 pdb tpr tpb tpa. 指定输入的坐标文件。
-n	index.ndx	Input, Opt.	Index file. 分子系统的索引文件。
-o	out.gro	Output, Opt.	Structure file: gro g96 pdb. 输出文件，即放进盒子里面的分子系统。
-mead	mead.pqr	Output, Opt.	Coordinate file for MEAD.
-bf	bfact.dat	Input, Opt.	Generic data file

3 其他选项

• -bt 选项和 -d 选项一起使用就可以构造盒子了，如果蛋白在模拟过程尺寸变化很大，那就用-box。

option	type	default	description
-[no]h	bool	no	Print help info and quit
-nice	int	0	Set the nicelevel
-[no]w	bool	no	View output xvg, xpm, eps and pdb files
-[no]ndef	bool	no	Choose output from default index groups
-bt	enum	triclinic	Box type for -box and -d: triclinic, cubic, dodecahedron or octahedron. 决定盒子的类型，triclinic是三斜晶的，cubic是立方体的，dodecahedron是十二面体的，octahedron是八面体的。
-box	vector	0 0 0	Box vector lengths (a,b,c). 自定义盒子大小，需要三个长度，即X、Y、Z三个方向的长度。
-angles	vector	90 90 90	Angles between the box vectors (bc,ac,ab)
-d	real	0	Distance between the solute and the box. 决定了盒子的尺寸，即盒子边缘距离分子边缘的距离。理论上此值应该大于0.9nm。
-[no]c	bool	no	Center molecule in box (implied by -box and -d)
-center	vector	0 0 0	Coordinates of geometrical center. 确定哪一部分分子放在盒子中心，如果和索引文件一起使用，可以非常详细的定义分子的位置。
-translate	vector	0 0 0	Translation. 平移分子，在X、Y、Z三个方向，随便移动。
-rotate	vector	0 0 0	Rotation around the X, Y and Z axes in degrees. 从 X Y Z三个方向转动分子。
-[no]princ	bool	no	Orient molecule(s) along their principal axes. 这个参数可以用来对齐分子，比如使分子沿X轴对齐。举一个例子吧，比如你想将分子中两个残基沿Y轴对齐，那么就在索引文件中将这俩个残基标记以下，然后使用-princ，根据提示走就能对齐分子啦。
-scale	vector	1 1 1	Scaling factor
-density	real	1000	Density (g/l) of the output box achieved by scaling
-[no]vol	bool	yes	Compute and print volume of the box
-[no]pbc	bool	no	Remove the periodicity (make molecule whole again)
-[no]grasp	bool	no	Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field
-rvdw	real	0.12	Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file
-sig56	real	0	Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2
-[no]vdwread	bool	no	Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field
-[no]atom	bool	no	Force B-factor attachment per atom
-[no]legend	bool	no	Make B-factor legend
-label	string	A	Add chain label for all residues

4 参见

• gromacs manual