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Which IC's to include in rtf?
#16791 01/24/08 05:27 AM
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diwakar Offline OP
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Hi all,
I was trying to build an entry for a residue in topology file. I am not clear on what are the IC's that should be included in the IC table? Is there a minimum number of entries for IC table? Is there any guideline or basic rules for writing IC table?
Further, one more thing that is not clear to me is how donor and acceptor atoms are decided for a residue and where this information is used by charmm?

Thanks
Diwakar

Re: Which IC's to include in rtf?
diwakar #16792 01/24/08 08:45 AM
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The IC table is *NOT* used for energy calculations (energy, minimize, dynamics). You only need it for analysis, or if you want to construct cartesian coordinates for parts of the system, or in more advanced situations where you want to change the conformation of your system. This answer was also given yesterday by Rick Venable to a similar question (with "IC" in the subject line). It is good practice to search the forums to see if the answer is already available before posting.

DONOr and ACCEptor specifications are not needed for any of the recent CHARMM force fields, but they are very handy if you want to analyze hydrogen bonding in your system - the COOR HBONd and COOR SECStructure commands rely on the donor/accptor information in the PSF. You would normally specify all atoms that can be hydrogen bond acceptors as ACCEptors (typically oxygens and nitrogens), and all hydrogens that can participate in hydrogen bonds as DONOrs (typically hydrogens bonded to oxygens and nitrogens). If the hydrogen bond concept is unclear to you, I suggest you consult an introducory chemistry text book.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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