Dear developers, first of all thank you for your work, the program is quite useful and interesting. I'm using it to perform molecular dynamics for small organic molecules but I have quite a few troubles. I was able to perform a MD in void, but I got this error when I try to analyze the energies, for both kinetic and potential.
File "C:\Program Files\Chimera 1.17.3\share\md\mdMovie.py", line 22, in <lambda>
name, lambda i, values=values: values[i-1])
Moreover, when I try to run a MD in water (I followed a tutorial on youtube to set up the system and balancing), it stops at the first step of minimization (after 2 days of running it didn't go further according to the log file). I used the Amber preparation (since Gestgeiger seems to not work for my molecules) integrated with AmberFF18SB or 99 that are the one that mostly worked out.
I don't think the problem is the calculation power of my machine since I've an Intel i5 processor with a GeForce MX230 and in the options I set up 4 processors.
Probably the troubles are just related to the fact that I'm working with small organic molecules instead of proteins?
Hoping to find some help/hint in your kind reply, whish a good day and good work,
Giovanni.
-- Giovanni Stelitano, PhD in Biomedical Science - BiochemistryDepartment of Biology and Biotechnology "L. Spallanzani"
University of Pavia
via Ferrata 9, Pavia, Italy
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