Re: [Rdkit-discuss] mol2 file with atom type that is suitable for amber

[Paul Emsley]

On 05/08/2020 19:44, Nikhil Maroli wrote:


I wanted to add atom types in mol2 file which is readable for 
amber/leap. Is it possible with rdkit?



I did some work on CCP4 and Amber atom types a few years ago and then 
converted to parm@Frosst (which I found to be a lot harder) but not to 
the point of correctness/publication (it was more than 90% coverage of 
the set suite though, IIRC).


https://github.com/pemsley/coot/blob/refinement/pyrogen/atom_types.py

Maybe it would be a useful start.


Paul.




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Re: [Rdkit-discuss] mol2 file with atom type that is suitable for amber

[Greg Landrum]

Hi Nikhil,

The RDKit cannot create mol2 files, so I’m afraid it can’t help at all.
Maybe take a look at openbabel or ambertools for this

-greg

On Wed, 5 Aug 2020 at 20:47, Nikhil Maroli  wrote:

> Dear all,
> I wanted to add atom types in mol2 file which is readable for amber/leap.
> Is it possible with rdkit?
>
> Here is an example
>
>  1 C1   4.2630-1.6530 0.0470 ca 1 MOL
> 0.00
>   2 C2   4.8250-0.3820 0.0880 ca 1 MOL
> 0.00
>   3 C3   4.0150 0.7380 0.0660 ca 1 MOL
> 0.00
>   4 C4   2.5090 0.6800 0.0600 ca 1 MOL
> 0.00
>   5 C5   2.2420-3.1690 0.1430 ca 1 MOL
> 0.00
>   6 C6   2.7860-1.8170 0.1380 ca 1 MOL
> 0.00
>   7 C7   1.9210-0.6670 0.1840 ca 1 MOL
> 0.00
>   8 C8   0.5270-0.7320 0.0450 ca 1 MOL
> 0.00
>   9 C9   0.3020-4.5350-0.4860 c2 1 MOL
> 0.00
>  10 C10  0.8110-3.3050-0.3020 ca 1 MOL
> 0.00
>  11 C11 -0.0470-2.1070-0.1620 ca 1 MOL
> 0.00
>
>
> Here ca, c2 represent atom types.
> --
> Regards,
> Nikhil Maroli
>
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