Big Molecule Generation

[aydinmirac]

Dear All,

Thanks for creating this tool.

I am trying to generate big molecules with surge tool. I know that the tool is working pretty good with small molecules but I am having some errors when I tried to create big ones that include roughly 130 atoms.

I tried to compile source code with bigger WORDSIZE (which was 64 during the compilation) but it gave the following error:

$ ./surge -o'spirometad.sdf' C61H46N2O5
>E surge : too many non-hydrogen atoms

Do you have any idea how I can fix this? Or do you have any suggestion for other tools to create big molecules?

Best regards,

[MehmetAzizYirik]

Dear All,

Thanks for creating this tool.

I am trying to generate big molecules with surge tool. I know that the tool is working pretty good with small molecules but I am having some errors when I tried to create big ones that include roughly 130 atoms.

I tried to compile source code with bigger WORDSIZE (which was 64 during the compilation) but it gave the following error:

$ ./surge -o'spirometad.sdf' C61H46N2O5 >E surge : too many non-hydrogen atoms

Do you have any idea how I can fix this? Or do you have any suggestion for other tools to create big molecules?

Best regards,

For the current version, the WORDSIZE can be set to maximum 64. The explanation is given in the Surge User Manual : "Surge can be compiled with -DWORDSIZE=64 if nautyW1.a is replaced by nautyL1.a. That will raise the limit on the number of non-hydrogen atoms from 32 to 64, but there are very few molecular formulas of that size for which the number of isomers is within reason. The number of bonds, ignoring hydrogen, is limited in 64 in any case."