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 Sat Sep 08 2012 - 08:30:02 PDT
