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Hello all,</div>
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There was a question about the H++ part of the amber tutorial and my notes that Travis sent out yesterday. </div>
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<span style="color: rgb(0, 0, 0); font-size: 12pt; font-family: calibri, arial, helvetica, sans-serif;">H++ is used to determine the protonation states of the two histidine residues within the RAMP1 protein: His75 should be double protonated (HIP) and HIS 97
should be protonated at the delta nitrogen (HID). </span><span style="color: rgb(0, 0, 0); font-family: calibri, arial, helvetica, sans-serif; font-size: 12pt; background: var(--white);">Your H++ output should match the tutorial. Once you have the file from
H++ you can transfer it back to the server and use vmd to visualize the protonation states. </span></div>
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<span style="caret-color:rgb(0, 0, 0);font-family:calibri, arial, helvetica, sans-serif;background-color:rgb(255, 255, 255);display:inline !important">Next you need to change the protonation states of the histidine residues and remove the CONECT lines. Note
these changes are to the file you uploaded to H++. The file that comes out of H++ is to know the protonation states; it is not the file you modify to run through tleap. </span></div>
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Best,<br>
Elizabeth</div>
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