Q1:
I am trying to set up your software package (libproteingeometry) on a lab
desktop. I having trouble during the Make step. After running for a while,
one of the packages is unable to link to the appropriate math header files,
causing make to exit with an error. I am able to understand some C++ coding,
but am not proficient enough to come up with a solution to this problem
independently. I would like to use your program, so is there anyway that you
can put me in contact with someone in your lab who might be able to help me
finish installing this software?

A1:
Apologies again for the delay. May I ask how many structures you plan on running? Customizing libprotgeometry for your machine’s settings may be pretty tricky, especially from our end. If you’re not running too many structures, I’d highly suggest using the Online version of this tool (assuming you’re calculating residue-level packing metrics), linked here:

http://www.molmovdb.org/cgi-bin/voronoi.cgi

Q2:
Unfortunately, I plan on using you program in some molecular dynamics analysis, so the number of structures would be on the order of thousands. I fee like this is too much to run on your server (unless your server has a MD analysis option that I missed, which would be great).

I can send you specific error messages I have upon trying to run the make command. Please let me know what would help you. I saw this error on a forum somewhere where it looked like the problem had been solved, but the solution was not posted.

A2:
Yes, please do send us specific error messages upon trying to run make, as well as any other error messages that you obtain. The more info we have, the better. We’ll try to sort things out. Also, what type of OS is your machine running?

Q3:
I run ubuntu 12.04. I’m pretty sure the system is a converted dell. i5 processor, with nvidia graphics card. I’ll send the error messages in the morning.