Dear Professor Dupradeau,
Thank you for usual and kind supports.
> You could use R.E.D. Server Dev. at
> http://q4md-forcefieldtools.org/REDServer-Development/
Yes, it is an excellent solution for me.
I will try it to build the parameters for res. with three terminal.
Thank you again.
Besides using R.E.D, I am still interested in how to use antechamber for this
purpose.
This does not mean I am a traditional Amber user, but
I believe that taking "basic steps" (preparing several input files etc)
is good for Amber beginners (including me)
to understand a concept of AMBER FF and computational chemistry.
I am wondering if you consider to give some advices for this point, too.
Yours sincerely,
IK
> -----Original Message-----
> From: FyD [mailto:fyd.q4md-forcefieldtools.org]
> Sent: Monday, May 05, 2014 3:47 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Prepareing branched residue
>
> 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.
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 06 2014 - 19:30:03 PDT
