Conversion of Mol2 file to mol2 file with atom type properties

[Nikhil Maroli]

Dear experts,

I need to use mol2 file with 2000 atoms in antechamber/amber. I need to convert the normal mol2 to antechamber generated type.

Here is tripose mole 2 type

# small_new

# Created by GaussView 6.0.16

#

#

#

@<TRIPOS>MOLECULE

Molecule Name

40 45

SMALL

NO_CHARGES

@<TRIPOS>ATOM

1 C1     4.2635    -1.6526     0.0469 C

2 C2     4.8253    -0.3821     0.0885 C

3 C3     4.0149     0.7380     0.0663 C

4 C4     2.5091     0.6797     0.0598 C

5 C5     2.2419    -3.1690     0.1429 C

6 C6     2.7859    -1.8170     0.1380 C

7 C7     1.9205    -0.6666     0.1839 C

8 C8     0.5272    -0.7317     0.0451 C

9 C9     0.3024    -4.5355    -0.4861 C

here is the mol2 for amber

@<TRIPOS>MOLECULE

Molecule

   40    45     1     0     0

SMALL

No Charge or Current Charge

@<TRIPOS>ATOM

      1 C1           4.2630    -1.6530     0.0470 ca         0 MOL       0.000000

      2 C2           4.8250    -0.3820     0.0880 ca         0 MOL       0.000000

      3 C3           4.0150     0.7380     0.0660 ca         0 MOL       0.000000

      4 C4           2.5090     0.6800     0.0600 ca         0 MOL       0.000000

      5 C5           2.2420    -3.1690     0.1430 cc         0 MOL       0.000000

      6 C6           2.7860    -1.8170     0.1380 ca         0 MOL       0.000000

      7 C7           1.9210    -0.6670     0.1840 ca         0 MOL       0.000000

      8 C8           0.5270    -0.7320     0.0450 ca         0 MOL       0.000000

      9 C9           0.3020    -4.5350    -0.4860 c2         0 MOL       0.000000

Here you can see there is representation of atom type such as ca, cc, and c2. Also, the numbering as C1,C2,C3...son on.

is there any way to do this is Mdanalysis.?

[Oliver Beckstein]

Hi Nikhil,

MDAnalysis does not have a mol2 writer. The docs suggest to use RDKIT, see https://docs.mdanalysis.org/1.0.0/documentation_pages/coordinates/MOL2.html

(In the upcoming 2.0 release we will have a direct interface to RDKIT but until then, there’s no simple way to do this in MDA 1.0.)

Oliver

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Oliver Beckstein

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