normal Molmaker.py issue

  • lfhjanssen
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7 years 1 month ago #7138 by lfhjanssen
Molmaker.py issue was created by lfhjanssen
Hi,

I'm currently parametrising a drug molecule. For this, I use automartini.py to obtain mappings for smaller fragments of the drug after which I "merge" them to obtain the full molecule. When I try to obtain a .gro file of the .itp file with the use of molmaker.py, it sometimes shows an "exploded" molecule as a result, even with just the standard output of auto martini as input (yes, I am fully aware that auto martini can give a .gro file as an output as well, but I wanted to see if it was my .itp file that was problematic. The gro output from automartini is fine).
Some other .itp of different fragments don't show any issues while others do.

Has anyone ever experienced this? Are there particular settings for molmaker.py to improve its functionality with Martini?

Thanks!
Laura

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7 years 1 month ago #7139 by peterkroon
Replied by peterkroon on topic Molmaker.py issue
Hi,

no script is magic, unfortunately. What flags do you give to molmaker? I've never used it, but looking at it you should at least provide -ff, -fuzzy, and -eps.

Peter

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