Dear Ikuo,
You could use R.E.D. Server Dev. at
http://q4md-forcefieldtools.org/REDServer-Development/
To create three connections between three elementary building blocks
you need to define specific charge constraints intra-mcc and/or
inter-mcc) applied during the charge fitting step.
You can find examples of such an approach in the REDDB database
http://q4md-forcefieldtools.org/REDDB/
and in tutorials available at
http://q4md-forcefieldtools.org/Tutorial/
Concerning CYX you could create a model of disulfide bridge such as
dipeptide_CH2S-SMe and apply an intra-mcc = 0 on the SMe group;
however to be checked with total charge value of the SMe group
obtained without this constraint...
R.E.D. Server Dev. performs charge derivation, force field library
building and force field parameter generation; key points here are
atom typing for molecular fragments and fragment fusion between the
different elementary building blocks involved in the procedure.
regards, Francois
> 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.
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Received on Mon May 05 2014 - 00:00:02 PDT
