About the output the mass information of all atoms of the force field in system.data for "all atoms"

[ysdlucky]

Hello！ I found a small problem.I successfully installed moltemplate on my computer which is windows 10 a few days ago.After that,I run a example on it .Its name is "alkane_chain_single" and the file path is “examples\all_atom\force_field_OPLSAA\alkane_chain_single”.

I got the system.data after running the moltemplate. Then I used the VMD to open this file. There was no problem in molecular configuration with VMD. But I found the mass information of all atoms that own to the force field in the system.data . It seems that this wouldn't affect the consequence of simulation.

I think it will be better if the data file just contains the mass information of the atoms of given system. Unfortunately I haven't learned python and how to use python yet. So I don't know how to deal with this small problem.I will start to to learn python and try to address this issue after I finish my current course.And when I'm done, I'll come back and give an answer.

Thank you!

ALEXysd.

[ysdlucky]

I suddenly find that jewettaij had given a way to solve this problem.So I decide to close this. Thank jewettaij ! Best wishes to you.

[jewettaij]

Hi ALEXysd You probably found the cleanup_moltemplate.sh script. That's by far the easiest the way to get around this problem. Unfortunately, I can imagine some situations where this script won't work very well. (Fortunately, these situations don't effect OPLSAA, DRIEDING, AMBER, or COMPASS users.) This "cleanup_moltemplate.sh" script is also very slow. For these reasons I don't run this automatically by default. I'm sorry that you had look for the solution to this problem online. I was hoping people would notice the README_remove_irrelevant_info.sh file. (Or this file.) Perhaps I should change the name of these files to make this information easier to find. Glad you solved your problem. Andrew