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Amber-MD / pytraj

Python interface of cpptraj
https://amber-md.github.io/pytraj
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calculated basepair matches in pytraj #1627

Open cloudella48 opened 1 year ago

cloudella48 commented 1 year ago

Hi there! I have already posted my issue before, I just noticed some further things I do not understand, so I am opening this new post. I want to calculate the major groove distances within pytraj for my simulation of a protein-DNA complex. For one or two baspairs I got some really wired output graphs. This is why I started checking on the basepairs directly. In the calculation pytraj is doing there is one basepair completely missing. I have checked with VMD and it seems correct to me, so I do not really understand why pytraj does not calculate the distances for this baspair? On top of this isuue I also get values = 0 random in some frames, but for all my different trajectories and I am asking myself how these are produced and if this might be a bug by pytraj? Here you can see how my putput plots look like, always with on value sticking out image I would be very greatful, if you could help me solving these two issues asap!

hainm commented 1 year ago

cc @drroe, just in case you know what's going on.

cloudella48 commented 1 year ago

Hi .. another questions you might be able to answer me apart from this wired issue explained above.. When one calculates major grooves, the values are around 19 to 20 like in the example given in the documentation. As the calculated value is said to be the major groove width (which normally is around 12 Angström) I wanted to ask, if it is rather the length of the groove? I am a bit lost here, also because it is not very well explained what exactly is calculated.. Is there another manual where one can see what exactly is calculated ?