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Luis Daniel Malagón

Is there any limit for the number of atoms to upload? and is there any way to label a H atom from methoxy group?

HI, First, I'm trying to upload a file with a polymethyl methacrylate chain which hold 9600 atoms around, but when I upload this file and push on "create data file", the tool does not generate anything, I mean, it seems like it was generating something but just gives box dimensions and does not any file, so, I was wondering if there is a limit of atoms because of this.

second: I'm studying intramolecular interaccions among this polymer, and it's great this tool can label each atom type by its geometry, it has been so helpful, but I need another label for H, because I need to know how is the interaction among only the H from the methoxy group and trigonal oxygen in the chain. by this I would like to know if i could make this of any way.

thank you.

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    Lorena Alzate-Vargas

    Hi Luis. The tool uses OpenBabel to handle the conversion and to retrieve information about the atom and bond types, for this reason there is limitation with the number of atoms it can received, and that is why the tool does not generate anything for the input structure you uploaded (I have tried with 3000 atoms and it works). About the hydrogen atom with a different label, the tool can not do it because the typing is done based on the forcefield in this case Dreiding and it is the force field that tell us what is the type (or label) for each atom, you could perhaps identify the atoms you need to label differently once the structure is generated by the tool and change it manually. 


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