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Missing donor specification in RTF
#38087 09/27/20 08:11 AM
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Ripplet Offline OP
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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

Re: Missing donor specification in RTF
Ripplet #38088 09/27/20 08:18 AM
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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
Re: Missing donor specification in RTF
lennart #38089 09/27/20 11:30 AM
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Ripplet Offline OP
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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

Re: Missing donor specification in RTF
Ripplet #38090 09/27/20 06:05 PM
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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

Re: Missing donor specification in RTF
rmv #38091 09/28/20 01:21 AM
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Ripplet Offline OP
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Thank you so much. I understand now.

Last edited by Ripplet; 09/28/20 01:31 AM.

Moderated by  lennart, rmv 

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