Dear Amber developers and users,
I am trying to prepare non-standard residue with three connections.
I guessed that the three connections can be set when we perform residuegen, and
Then prepared the input file shown below, where three "SEP_BOND" commands are
used.
_________________________________________________________________
INPUT_FILE ASE_byIK.ac
CONF_NUM 1
ESP_FILE MS1_a.esp
SEP_BOND N C12
SEP_BOND OG C9
SEP_BOND C N23
NET_CHARGE 0
PREP_FILE: ASE_byIK.prepin
RESIDUE_FILE_NAME: ASE
RESIDUE_SYMBOL: ACCSER.RES
_________________________________________________________________
However, the prepin file is not generated properly.
Cannot we use "SEP_BOND" command over 2 connect definition?
If so, how was CYX generated?
I am most grateful if you give me an advice for this problem.
Yours sincerely,
Ikuo KURISAKI
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Received on Thu May 01 2014 - 23:00:02 PDT
