读入chg文件后，top文件生成时闪退

sunchao

老师，在使用sobtop过程中，先利用Multiwfn得到了chg文件，然后读入sobtop，在按照步骤获取top文件，
到 2（指认GAFF原子类型）时，闪退，不知道什么原因
这是我的mol2文件和chg文件
请各位老师帮我看看有什么错误？

sunchao

sobereva 发表于 2024-5-21 02:52
没有发现你提到的问题，至少是对于sobtop目前官网上的最新版来说。
sobtop启动后输入的命令和输出都粘贴在 ...

谢谢老师，我重新下一个最新版本试试

sobereva

没有发现你提到的问题，至少是对于sobtop目前官网上的最新版来说。
sobtop启动后输入的命令和输出都粘贴在下面了，我输入的加粗表示。可见GAFF原子类型已经成功指认了
照着检查

Sobtop: A tool of generating forcefield parameters and GROMACS topology file
Website: http://sobereva.com/soft/sobtop
Developed by Tian Lu (sobereva@sina.com)
Beijing Kein Research Center for Natural Sciences (http://www.keinsci.com)
Version 1.0(dev3.2)  First release: 2024-Feb-17

Input path of .mol2/pdb/pqr file, e.g. D:\lovelive\Liella\Sumire_Heanna.mol2
Note: For common molecule systems, .mol2 should be used
C:\Users\sober\Desktop\AC.mol2

Loading atom information and connectivity from .mol2 file...

Generating neighbouring list...

Loaded information and connectivity (coordinates in Angstrom):
  Atom     X       Y       Z      Charge    Bonds to
    1C   -0.221  -0.002  -0.000   0.00000     2O      3O      4C
    2O   -0.804   1.106   0.000   0.00000     1C
    3O   -0.697  -1.160   0.000   0.00000     1C
    4C    1.354   0.053   0.000   0.00000     1C      5H      6H      7H
    5H    1.740  -0.477   0.880   0.00000     4C
    6H    1.740  -0.477  -0.880   0.00000     4C
    7H    1.728   1.082  -0.000   0.00000     4C

Generating angles and dihedrals according to connectivity...
Determining bond list...
Number of bonds:         6
Determining angle list...
Number of angles:         9
Determining dihedral list...
Number of dihedrals:         6

     ============================== Sobtop ==============================
-2 Set scale factor for derived force constants, current: Default
-1 Select method for deriving rigid parameters: mSeminario
0 Exit program
1 Generate GROMACS topology file
2 Generate GROMACS .gro file
3 Generate GROMACS .rtp file
4 Generate .gjf file (for visualizing connectivity in GaussView)
5 Derive rigid parameter for specific bond/angle/dihedral
6 Derive rigid parameters for all bonds, angles and dihedrals
7 Assign atomic charges
10 Other functions
C:\Users\sober\Desktop\AC.chg
Loading is successful. Current atom charges:
    1C   0.8252166750
    2O  -0.7795267861
    3O  -0.7839295826
    4C  -0.2898867089
    5H   0.0093754675
    6H   0.0093754675
    7H   0.0093754675
Sum of atomic charges: -1.0000000001

Because "ichggeom" in sobtop.ini is 1, therefore the current geometry has been replaced with that in .chg file

     ============================== Sobtop ==============================
-2 Set scale factor for derived force constants, current: Default
-1 Select method for deriving rigid parameters: mSeminario
0 Exit program
1 Generate GROMACS topology file
2 Generate GROMACS .gro file
3 Generate GROMACS .rtp file
4 Generate .gjf file (for visualizing connectivity in GaussView)
5 Derive rigid parameter for specific bond/angle/dihedral
6 Derive rigid parameters for all bonds, angles and dihedrals
7 Assign atomic charges
10 Other functions
1

Now please use the options in this interface to assign atom types. When atom types for all atoms are assigned, then you can use option 0 to enter next step. For convenience, you can also use option 2 to assign GAFF and then UFF atom types and directly go to next step

     7 atoms do not have atom type currently

-2 Load all atom types from a file
-1 Export all current atom types to a file
1 Assign UFF atom types for all undetermined atoms
2 Assign GAFF atom types first and then UFF, then go to next step
3 Assign GAFF atom types as much as possible
4 Assign AMBER atom types as much as possible
5 Assign atom types according to the rule in assign_AT.dat file
6 Manually set atom type for selected atoms
7 Make all atom types to undetermined state
9 Show all current atom types on screen
2
Running: atomtype -i "C:\Users\sober\Desktop\AC.mol2" -f mol2 -o MOL.ac -d ATOMTYPE_GFF.DEF ...
Deleting ATOMTYPE.INF MOL.ac
GAFF atom types are assigned for      7 atoms
UFF atom types are assigned for      0 atoms

Current atom types and meaning:
    1C : c          Sp2 C carbonyl group
    2O : o          Oxygen with one connected atom
    3O : o          Oxygen with one connected atom
    4C : c3         Sp3 C
    5H : hc         H bonded to aliphatic carbon without electrwd. group
    6H : hc         H bonded to aliphatic carbon without electrwd. group
    7H : hc         H bonded to aliphatic carbon without electrwd. group

Well, LJ parameters of all atoms can be found in LJ_param.dat. Now we go to next stage

How to generate bonded parameters for the topology file?
Note: "prebuilt" parameters in this context refer to those in bonded_param.dat
0 Return
1 Without bonded parameters
2 All bonded parameters are determined by mSeminario method
3 Prebuilt bonded parameters if possible, missing ones are supplemented by mSeminario method
4 Same as option 3, but missing ones are arbitrarily guessed
5 Bonded parameters related to selected atoms (usually rigid region) are determined by mSeminario method, others use prebuilt bonded parameters, then missing ones are supplemented by mSeminario method
6 Same as option 5, but missing ones are arbitrarily guessed
7 All bond and angle parameters are determined by mSeminario method, others use prebuilt bonded parameters, then missing ones are supplemented by mSeminario method