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Topic: problem following the protocol (Read 21429 times)
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albezg
Isostatic
Posts: 42
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I am trying to follow these instructions: http://flexweb.asu.edu/software/first/first_protocols/largeScaleMotionInIg.pdfHowever, at step 7 clusters of interest remain separated. I have also tried to use both options -phin and -phout at the same time and I noticed that the artificially added bonds with 6 bars get reset to 2 bars. I suppose that added hydrogen bonds do not go through such validity test, so I used -hbout and -hbout instead -phout and -phin. This time bonds remained at 6 bars and the clusters got connected. Nevertheless, The size of this combined cluster is still small (RC3). What should I do? |
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Brandon
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albezg,
I'm looking into this now. Can you tell me, did you use the WhatIf server to add hydrogens, or some different program?
Brandon
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albezg
Isostatic
Posts: 42
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Yes, it was whatif. Right now I tried mol probity and it was enough to add 1 hydrogen bond(6 bars) to connect the clusters into RC1
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