Dear Amber Experts:
If I do an rms fitting using Ptraj to a box filled with water, mask being the backbone atoms of the protein, the water must have been transformed in the same way (same matrix). This may cause some water to be out of the original box. Will Ptraj automatics image these water molecules back into the box or not?
Another question. Is there a way to extract the information of the box? Like the coordinates of the vertex, if the side is paralleled with the axis.
Thank you.
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Received on Tue Nov 06 2012 - 23:30:03 PST
