Dear IK,
>> 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.
The problem is that I do not use & I do not know well Antechamber; I
even barely use it because we develop the q4md-forcefield tools, where
the central point is charge derivation involving multiple molecules
multiple conformations and multiple orientations: the main idea here
is to develop general & reproducible charge values for MD simulation.
My understanding of Antechamber (one can correct me if I am wrong) is
more how to quickly derive 'reasonable' charge values: I do not
support this idea.
Concerning the problem you reported and if you do not get any answer
from the Amber mailing list this might mean the reported feature
simply does not work: all programs have bugs... In my opinion only
'RED' proposes approaches that do handle complex sets of mep-based
charge constraints required to generate molecular fragments and/or
complex sets of fragments.
regards, Francois
>> -----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.
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Received on Wed May 07 2014 - 12:30:02 PDT
