The Molecular Graphics Laboratory Forum

Hello,

I have prepared a ligand in mol2 format with all charges and hydrogens correctly added. When I merge the non-polar hydrogens (Edit>Hydrogens>Merge Non polar), the partial charges get completely messed up and the total charge is no more an integer. Typically, a C-H with partial charges of 0.10 and 0.03 becomes a merged C with a charge of 0.16! Does anybody know where the problem may come from?

Thanks,
Nicolas

I finally figured out what the problem was. For some reason, the residue name was not assigned correctly in the initial mol2 file. It was "<1>" instead instead of a regular 3-letter name. I changed the mol2 manually, then converted it in the pqr format with VMD and finally opened the .pqr in AutodockTools (the direct opening of the mol2 file generates errors). I merged the non-polar hydrogens, checked the charges; everything was OK.

Hi, I am Shrek Wang, a student in WuHan University of Technology, China.
I am starting to use AutoDock.
I am concerning that how you can find the error of the mol2 file format. Did you using some software which can detect the error?
I will appraciate it, if you share your experience with me. Thank you!
Shrek

Wang, from what I understand it was a file error and not a program error. Am I correct, Nicolas? There do seem to be some flaws with AutoDock at this time, at least I'm having some trouble, so it would be nice to see an updated version soon.

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Hi, Enzymatic8.

I am glad to see your answer. You know that some of the PDB/mol2 files are not standard. I am wondering how to find the errors in the files? maybe through some softwares? Maybe you can tell me something about it.

I am also looking forward to the new version which can detect the error of the input file automatically.

Thanks,
Shrek