Dear all,
I have a big structure (~2000 atoms) to use in amber which is non-standard for amber forcefield.
I wanted to convert syble mol2 file to amber type which shows amber atom types.
Any suggestions?
Syble format
1 C 0.0116 0.0237 1.1227 C.2 1 GRA 0.0000 BACKBONE
2 C -0.4325 0.6090 2.3024 C.2 2 GRA 0.0000 BACKBONE
3 C 0.0028 1.8719 2.6594 C.2 3 GRA 0.0000 BACKBONE
4 C 0.9108 2.7158 1.8024 C.2 4 GRA 0.0000 BACKBONE
5 C 1.2320 0.1781 -1.0869 C.2 5 GRA 0.0000 BACKBONE
6 C 0.8309 0.8136 0.1618 C.2 6 GRA 0.0000 BACKBONE
7 C 1.2428 2.1568 0.4789 C.2 7 GRA 0.0000 BACKBONE
8 C 2.1898 2.8783 -0.2611 C.2 8 GRA 0.0000 BACKBONE
9 C 2.9745 0.1093 -2.8142 C.2 9 GRA 0.0000 BACKBONE
10 C 2.4506 0.7525 -1.7572 C.2 10 GRA 0.0000 BACKBONE
antechamber generated mol2
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
10 C10 0.8110 -3.3050 -0.3020 cc 0 MOL 0.000000
Martin Klvana antechamber cant process 2000 atoms. we have generated resp charges/parameters for small units. But now we have to make the bigger structure to mol2 format of the antechamber.
Like aromatic carbon as ca, carboxy as c in the atom type column
If dividing the big structure into smaller units is not feasible, i would generate the mol2 file manually (i.e., with a script).
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