调整Gromacs拓扑文件（.top/.itp）中的原子序号及相应的bonds等信息，主要用于非标准残基(Non-standard residue)的处理
根据李继存老师的这篇博文编写脚本：https://jerkwin.github.io/2022/01/06/%E8%87%AA%E5%86%99%E8%84%9A%E6%9C%AC%E5%88%9B%E5%BB%BA%E9%9D%9E%E6%A0%87%E5%87%86%E6%AE%8B%E5%9F%BA%E8%9B%8B%E7%99%BD%E7%9A%84GROMACS%E6%8B%93%E6%89%91/
下载cgtop
sudo cp ./cgtop /usr/local/bin暂未编译
demo.top 点击展开
;
; Example topology file
;
; The force-field files to be included
#include "amber99.ff/forcefield.itp"
[ moleculetype ]
; name nrexcl
Urea 3
[ atoms ]
1 C 1 URE C 1 0.880229 12.01000 ; amber C type
2 O 1 URE O 2 -0.613359 16.00000 ; amber O type
3 N 1 URE N1 3 -0.923545 14.01000 ; amber N type
4 H 1 URE H11 4 0.395055 1.00800 ; amber H type
5 H 1 URE H12 5 0.395055 1.00800 ; amber H type
6 N 1 URE N2 6 -0.923545 14.01000 ; amber N type
7 H 1 URE H21 7 0.395055 1.00800 ; amber H type
8 H 1 URE H22 8 0.395055 1.00800 ; amber H type
[ bonds ]
1 2
1 3
1 6
3 4
3 5
6 7
6 8
[ dihedrals ]
; ai aj ak al funct definition
2 1 3 4 9
2 1 3 5 9
2 1 6 7 9
2 1 6 8 9
3 1 6 7 9
3 1 6 8 9
6 1 3 4 9
6 1 3 5 9
[ dihedrals ]
3 6 1 2 4
1 4 3 5 4
1 7 6 8 4
[ position_restraints ]
; you wouldn't normally use this for a molecule like Urea,
; but we include it here for didactic purposes
; ai funct fc
1 1 1000 1000 1000 ; Restrain to a point
2 1 1000 0 1000 ; Restrain to a line (Y-axis)
3 1 1000 0 0 ; Restrain to a plane (Y-Z-plane)
[ dihedral_restraints ]
; ai aj ak al type phi dphi fc
3 6 1 2 1 180 0 10
1 4 3 5 1 180 0 10
; Include TIP3P water topology
#include "amber99.ff/tip3p.itp"
[ system ]
Urea in Water
[ molecules ]
;molecule name nr.
Urea 1
SOL 1000
# 删除原子序号5-10的原子（包括5和10），原文件为demo.top，输出结果到demo_del.top
# 以下两个命令效果一致
cgtop del -s 5 -e 10 -p demo.top -o demo_del.top
cgtop del --start 5 --end 10 --top demo.top --out demo_del.top
cgtop del 执行结果
;
; Example topology file
;
; The force-field files to be included
#include "amber99.ff/forcefield.itp"
[ moleculetype ]
; name nrexcl
Urea 3
[ atoms ]
1 C 1 URE C 1 0.880229 12.01000 ; amber C type
2 O 1 URE O 2 -0.613359 16.00000 ; amber O type
3 N 1 URE N1 3 -0.923545 14.01000 ; amber N type
4 H 1 URE H11 4 0.395055 1.00800 ; amber H type
[ bonds ]
1 2
1 3
3 4
[ dihedrals ]
; ai aj ak al funct definition
2 1 3 4 9
[ dihedrals ]
[ position_restraints ]
; you wouldn't normally use this for a molecule like Urea,
; but we include it here for didactic purposes
; ai funct fc
1 1 1000 1000 1000 ; Restrain to a point
2 1 1000 0 1000 ; Restrain to a line (Y-axis)
3 1 1000 0 0 ; Restrain to a plane (Y-Z-plane)
[ dihedral_restraints ]
; ai aj ak al type phi dphi fc
; Include TIP3P water topology
#include "amber99.ff/tip3p.itp"
[ system ]
Urea in Water
[ molecules ]
;molecule name nr.
Urea 1
SOL 1000
# 提取原子序号5-10的原子（包括5和10），原文件为demo.top，输出结果到demo_del.top
# 以下两个命令效果一致
cgtop extra -s 5 -e 10 -p demo.top -o demo_extra.top
cgtop extra --start 5 --end 10 --top demo.top --out demo_extra.topcgtop extra 执行结果
;
; Example topology file
;
; The force-field files to be included
#include "amber99.ff/forcefield.itp"
[ moleculetype ]
; name nrexcl
[ atoms ]
5 H 1 URE H12 5 0.395055 1.00800 ; amber H type
6 N 1 URE N2 6 -0.923545 14.01000 ; amber N type
7 H 1 URE H21 7 0.395055 1.00800 ; amber H type
8 H 1 URE H22 8 0.395055 1.00800 ; amber H type
[ bonds ]
1 6
3 5
6 7
6 8
[ dihedrals ]
; ai aj ak al funct definition
2 1 3 5 9
2 1 6 7 9
2 1 6 8 9
3 1 6 7 9
3 1 6 8 9
6 1 3 4 9
6 1 3 5 9
[ dihedrals ]
3 6 1 2 4
1 4 3 5 4
1 7 6 8 4
[ position_restraints ]
; you wouldn't normally use this for a molecule like Urea,
; but we include it here for didactic purposes
; ai funct fc
[ dihedral_restraints ]
; ai aj ak al type phi dphi fc
3 6 1 2 1 180 0 10
1 4 3 5 1 180 0 10
; Include TIP3P water topology
#include "amber99.ff/tip3p.itp"
[ system ]
[ molecules ]
;molecule name nr.
该部分由于修改的复杂性采用csv输入和纯命令行输入的方式来达不同需求的修改，可以利用WPS或者Microsoft Office来编写csv文件
- csv输入
demo.csv
2,24
3,25
4,26
第一列为原始index，第二列为新的index，程序会自动更新bonds等项下的数字
# 以下两个命令效果一致
cgtop change -c demo.csv -p demo.top -o demo_change.top
cgtop change --csv demo.csv --top demo.top --out demo_change.topcgtop change 执行结果
;
; Example topology file
;
; The force-field files to be included
#include "amber99.ff/forcefield.itp"
[ moleculetype ]
; name nrexcl
Urea 3
[ atoms ]
1 C 1 URE C 1 0.880229 12.01000 ; amber C type
24 O 1 URE O 24 -0.613359 16.00000 ; amber O type
25 N 1 URE N1 25 -0.923545 14.01000 ; amber N type
26 H 1 URE H11 26 0.395055 1.00800 ; amber H type
5 H 1 URE H12 5 0.395055 1.00800 ; amber H type
6 N 1 URE N2 6 -0.923545 14.01000 ; amber N type
7 H 1 URE H21 7 0.395055 1.00800 ; amber H type
8 H 1 URE H22 8 0.395055 1.00800 ; amber H type
[ bonds ]
1 24
1 25
1 6
25 26
25 5
6 7
6 8
[ dihedrals ]
; ai aj ak al funct definition
24 1 25 26 9
24 1 25 5 9
24 1 6 7 9
24 1 6 8 9
25 1 6 7 9
25 1 6 8 9
6 1 25 26 9
6 1 25 5 9
[ dihedrals ]
25 6 1 24 4
1 26 25 5 4
1 7 6 8 4
[ position_restraints ]
; you wouldn't normally use this for a molecule like Urea,
; but we include it here for didactic purposes
; ai funct fc
1 1 1000 1000 1000 ; Restrain to a point
24 1 1000 0 1000 ; Restrain to a line (Y-axis)
25 1 1000 0 0 ; Restrain to a plane (Y-Z-plane)
[ dihedral_restraints ]
; ai aj ak al type phi dphi fc
25 6 1 24 1 180 0 10
1 26 25 5 1 180 0 10
; Include TIP3P water topology
#include "amber99.ff/tip3p.itp"
[ system ]
Urea in Water
[ molecules ]
;molecule name nr.
Urea 1
SOL 1000
- 纯命令行输入 暂未开发
注意：程序输出不会覆盖文件，会在原有文件上增加内容，如果输出文件有误，请删除原来的输出文件再重新执行命令！！！
使用Dart编写主要目的是方便后面使用Flutter编写GUI，权当练手了。