Gromacs/Make ndx
来自KlniuWiki
此命令实际上是make_ndx.
1 用法
This post explains how to efficiently use the GROMACS tool make_ndx to define atomic subgroups of a simulation system for subsequent analysis.
There are: 0 OTHER residues There are: 960 PROTEIN residues There are: 0 DNA residues Analysing Protein... 0 System : 14571 atoms 1 Protein : 14571 atoms 2 Protein-H : 7479 atoms 3 C-alpha : 960 atoms 4 Backbone : 2880 atoms 5 MainChain : 3844 atoms 6 MainChain+Cb : 4730 atoms 7 MainChain+H : 4744 atoms 8 SideChain : 9827 atoms 9 SideChain-H : 3635 atoms nr : group ! 'name' nr name 'splitch' nr Enter: list groups 'a': atom & 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char "name": group 'case': case sensitive 'q': save and quit
r 1 - 355
Found 5467 atoms with res.nr. in range 1-355 10 r_1-355 : 5467 atoms
0 System : 14571 atoms 1 Protein : 14571 atoms 2 Protein-H : 7479 atoms 3 C-alpha : 960 atoms 4 Backbone : 2880 atoms 5 MainChain : 3844 atoms 6 MainChain+Cb : 4730 atoms 7 MainChain+H : 4744 atoms 8 SideChain : 9827 atoms 9 SideChain-H : 3635 atoms 10 r_1-355 : 5467 atoms
name 10 SUB_H
10 & 2
Copied index group 10 'SUB_H' Copied index group 2 'Protein-H' Merged two groups with AND: 5467 7479 -> 2783 11 SUB_H_&_Protein-H : 2783 atoms
name 11 SUB_H_HEAVY
0 System : 14571 atoms 1 Protein : 14571 atoms 2 Protein-H : 7479 atoms 3 C-alpha : 960 atoms 4 Backbone : 2880 atoms 5 MainChain : 3844 atoms 6 MainChain+Cb : 4730 atoms 7 MainChain+H : 4744 atoms 8 SideChain : 9827 atoms 9 SideChain-H : 3635 atoms 10 SUB_H : 5467 atoms 11 SUB_H_HEAVY : 2783 atoms 12 SUB_H_BB : 1065 atoms
splitch 1
Found 4 chains 1: 5467 atoms (1 to 5467) 2: 5467 atoms (5468 to 10934) 3: 1816 atoms (10935 to 12750) 4: 1821 atoms (12751 to 14571)
del 5-13
0 System : 14571 atoms 1 Protein : 14571 atoms 2 Protein-H : 7479 atoms 3 C-alpha : 960 atoms 4 Backbone : 2880 atoms 5 SUB_H_BB : 1065 atoms 6 SUB_J_BB : 1065 atoms 7 SUB_M_BB : 375 atoms 8 SUB_L_BB : 375 atoms
r 886 905
9 r_886_905 : 40 atoms
splitat 9
0 System : 14571 atoms 1 Protein : 14571 atoms 2 Protein-H : 7479 atoms 3 C-alpha : 960 atoms 4 Backbone : 2880 atoms 5 SUB_H_BB : 1065 atoms 6 SUB_J_BB : 1065 atoms 7 SUB_M_BB : 375 atoms 8 SUB_L_BB : 375 atoms 9 r_886_905 : 40 atoms 10 r_886_905_N_13464 : 1 atoms 11 r_886_905_H_13465 : 1 atoms ... 32 r_886_905_CM_13486 : 1 atoms 33 r_886_905_HM1_13487 : 1 atoms 34 r_886_905_HM2_13488 : 1 atoms 35 r_886_905_HM3_13489 : 1 atoms ... 45 r_886_905_CG_13770 : 1 atoms 46 r_886_905_OD1_13771 : 1 atoms 47 r_886_905_OD2_13772 : 1 atoms 48 r_886_905_C_13773 : 1 atoms 49 r_886_905_O_13774 : 1 atoms
del 9-31
del 13 -21
del 16-17
0 System : 14571 atoms 1 Protein : 14571 atoms 2 Protein-H : 7479 atoms 3 C-alpha : 960 atoms 4 Backbone : 2880 atoms 5 SUB_H_BB : 1065 atoms 6 SUB_J_BB : 1065 atoms 7 SUB_M_BB : 375 atoms 8 SUB_L_BB : 375 atoms 9 r_886_905_CM_13486 : 1 atoms 10 r_886_905_HM1_13487 : 1 atoms 11 r_886_905_HM2_13488 : 1 atoms 12 r_886_905_HM3_13489 : 1 atoms 13 r_886_905_CG_13770 : 1 atoms 14 r_886_905_OD1_13771 : 1 atoms 15 r_886_905_OD2_13772 : 1 atoms
2 参考文献
- Theodros Zelleke. How to use make_ndx in GROMACS[EB/OL], 2011-02-05. [2011-08-07]. http://www.zelleke.com/2011/02/how-to-use-make_ndx-in-gromacs/.
