Thanks Francois for your help , I guess I am on the track now. RED is a bit time consuming but due to what you said it worths it.
A quick unrelated question: What is the latest antechamber version with mopac?
Thank you,
Rezvan
On Sep 8, 2012, at 10:10 AM, FyD wrote:
> Dear Rezvan,
>
>> I followed your suggestion and tried R.E.D. I basically don't understand what is going on in Fig 1 of the tutorials.
>
> So we missed the role of this image ;-)
>
>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
>>> or
>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#1
>
> This image tries to summarize the central role of a force field library (or a set of force field libraries in the mol2 (or mol3 file format)) when one wishes to run MD simulations at q4md-forcefieldtools.org: You start from PDB input file(s), where atom and residue names are (more or less correctly) defined (by the user). You execute Ante_R.E.D. to generate P2N file(s) from these PDB input file(s). From the P2N file(s) mol2 files are generated by R.E.D. Then, these mol2 files are loaded in LEaP (& associated with a selected force field and other FF libraries; atom types are also added in LEaP at this stage: see below) to generate the prmtop/prmcrd files for a complex molecular system; these prmtop/prmcrd files are directly used for MD simulations using sander/pmemd (AMBER) or indirectly used for MD simulations using CHARMM.
>
>> Are these parameters, AMBER parameters or CHARMM's?! Does it mean till producing Mol2/Mol3 files nothing different is going on?!
>
> mol2 vs mol3: see http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
>
> mol2 file: see http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
>
> I would like to underline that the 'savemol2' command has been incorporated in LEaP by C. Cezard at q4md-forcefieldtools.org; we also have developed the mol3 file format.
>
>> 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.
>
> The mol2 files generated by R.E.D. does not contain any FF parameter!
>
> savemol2 unit mol2filename option
> -> utility of the 'option' add or not add the FF atom types of a given force field
>
> These FF atom types are added using a LEaP script...
> See all the projects in R.E.DD.B. for instance W-46:
> http://q4md-forcefieldtools.org/REDDB/projects/W-46/
> & its LEaP script:
> http://q4md-forcefieldtools.org/REDDB/projects/W-46/script1.ff
> where the FF atom types ... for the Cornell et al. FF are defined.
>
> I am sure you can invent your own story for mol2 vs mol3 vs rtf file formats and AMBER vs CHARMM ;-)
>
> The new version of R.E.D. (we are working on) will handled many new features (& the P2N & mol2 files will not be used anymore).
>
>> This is exactly what I am trying to do:
>
> I understand ;-)
>
>> 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.
>
> "find the AMBER parameters"? I would answer you have to validate the AMBER parameters in the CHARMM context...
>
> regards, Francois
>
>
>> 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 14 2012 - 10:00:05 PDT
