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 Missing donor specification in RTF
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Joined: Jan 2007
Posts: 63
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Dear all, First question: If the donor specification in RTF is missing, can we add them in an anlysis file? If yes, how? Second question: I found there are type H in the RTF file, while when I used "select type H end" and got the result of "0 atom has been selected"? Thank you very much for your kind help. Best Wishes, Ripplet
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 Re: Missing donor specification in RTF
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Joined: Sep 2003
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DONOR/ACCEPTOR ADD (hbonds.info) The TYPE is the name of the atom in the RTF, whereas the chemical identiry of the atom is referred to as CHEM.
Lennart Nilsson Karolinska Institutet Stockholm, Sweden
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 Re: Missing donor specification in RTF
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Thank you very much! For the second question, I still feel confused. For example, I saw there are type H for hydrogens in Cys secification as following, the type of the hydrogen connected to nitrogen is H, but when I use "select type H end", I could not select any atom. RESI CYS 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N
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 Re: Missing donor specification in RTF
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Joined: Sep 2003
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For this atom, you can use either SELE TYPE HN END or SELE CHEM H END; note that other hydrogens besides the backbone amide HN also correspond to CHEM H, such as protons on side chain NH2 or OH. The selection TYPE HN is more specific, while CHEM H is more general as it can be used for other atom TYPEs.
Rick Venable computational chemist
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 Re: Missing donor specification in RTF
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Thank you so much. I understand now.
Last edited by Ripplet; 09/28/20 01:31 AM.
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