Dear Francois,
I followed your suggestion and tried R.E.D. I basically don't understand what is going on in Fig 1 of the tutorials.
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
> or
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#1
Are these parameters, AMBER parameters or CHARMM's?! Does it mean till producing Mol2/Mol3 files nothing different is going on?! Then how these files turn into "rtf" format? Is it just rtf format with AMBER parameters or CHARMM parameters. As you know for sure these two force fields have totally different parameters.
This is exactly what I am trying to do:
Find the AMBER parameters for an antibiotic which is inside a ribosome. I have AMBER parameters for ribosome in "CHARMM format" (because I run MD in NAMD and it needs CHARMM format). I need to have something similar for the antibiotic. Basically AMBER parameters, but once I got them I have to change the format to "CHARMM"'s.
Hopefully I could explain clearly what my problem is.
Thank you very much for your time and attention!
Cheers,
Rezvan
On Sep 5, 2012, at 2:15 AM, FyD wrote:
> Dear Rezvan,
>
>> I want to have the parameters for antibiotics bonded to ribosomes. I was wondering if I have to use ANTECHAMBER?
>
> You can use Antechamber and/or R.E.D. (or R.E.D. Server) at http://q4md-forcefieldtools.org.
>
> I would like to suggest you to use R.E.D. (or R.E.D. Server). If your antibiotics are connected through a bond to a larger system, I suggest you twice to use R.E.D. ;-) as you will have to define charge constraints during the charge fitting step.
>
>> I mean shall I produce the parameters myself?
>
> If they are not available: Yes
>
>> Have it been done before? Do parameters for antibiotics already exist in a par/topology file?
>
> In general you start from a PDB file and you generate a FF library (off, mol2 or prep format) using R.E.D. or Antechamber for your molecule; you load this new FF library in the LEaP program (with the FF you wish to use) and create the prmtop/prmcrd files for your entire molecular system for MD simulation.
>
> Concerning using R.E.D. see:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
> or
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#1
>
>> By the way, I am not still sure. To use the ANTECHAMBER do I need to buy the AMBER program?!
>
> Antechamber and R.E.D. are provided at no cost; R.E.D. is free. Antechamber is in the AmberTools (most of these tools are free).
>
> regards, Francois
>
>
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Received on Fri Sep 07 2012 - 19:00:03 PDT
