Dear Rezvan,
> 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.
This is normal because you use a QM program and the optimization
threshold defined is tight.
You could use R.E.D. Server as well although these days it is down for
upgrade...
> A quick unrelated question: What is the latest antechamber version
> with mopac?
I think the semi-emp. 'sqm' tool is used in the AmberTools by now.
regards, Francois
>
> 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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>
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Sat Sep 15 2012 - 06:00:03 PDT
