Please start a new thread for a new question rather than replying to an old one! Can a site admin please move the previous post and this post into a new thread?

Originally Posted By: Ascaris
I do have a question about submitting molecules to the paramchem website. The instructions state that molecules must be in the mol2 format. This, from what I've been able to determine, is a proprietary format. Is SYBYL required? From this post and searches of the charmm documentation, I gather that (a) it is not but (b) CHARMM will not save in this format. Are these conclusions correct?
Thank you for your interest. The mol2 format was developed by the company Tripos (the producer of Sybyl), but they have included a full description of the format in their documentation for as long as I can remember, and have never discouraged other companies from using it as far as I know (just google "mol2 format" and the first link will let you download a pdf document with the full mol2 specification from the Tripos website). Together with the fact that they were one of the first actors in the field to develop a flexible molecular database format for drug discovery, this caused the mol2 format to become a de facto standard; mol2 is more widely supported than any other format and it is precisely for this reason that we chose it as our input format.

Originally Posted By: Ascaris
Assuming that they are, it appears that VMD may be able to save in this format. Can it do this successfully for purposes of submission to the paramchem website?
Be a scientist - try it! wink If VMD complies with the aforementioned mol2 standard, it should work (and these guys are pretty competent so I expect it will).