Re: how to use measure hbonds to calculate occupancy of all hbonds in simulation?

From: lnubiofox (lnubiofox_at_163.com)
Date: Wed May 16 2007 - 09:57:51 CDT

Dear Dong Luo, Thank you very much for your script which help me a lot.It seems that you have solve the problem which puzzled me for a long time. I would like to express my thank to you and cite the script named hbond_occupancy in Acknowledgement of our paper which will be published soon.By the way,I suggest you submit your script to the vmd script library so that more users will benefit. However,there is still a question: I run the script and got a file in the appendix,but the result confuses me.For example ,there are many ARG35-ASP77s,what's the meaming of it? Is this a bug of the script or it means there are many H-bonds between ARG35-ASP77? If the latter,then how about divide them into main chain-main chain interaction, side chain-side chain interaction and main chain-side chain interaction?In other words,how to calculate main chain-main chain Hbonds,etc.? Use the atomselect command of vmd ? I highly appreciate your efforts on my question.Thank you again for your kind assistance and looking forward to your reply. With best regards, Yuan Liu Liaoning university ShenYang,P.R.China
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