Dear Francois,
Thanks for your reply. This is the RED one I actually used. The point is that I already had part of the project done with ANTECHAMBER and I wanted to just combine a better charge derivation method with it. I am planning to do another homogenous run later and write that tutorial we discussed :)
Thanks for reply,
Mohammad
On Aug 30, 2014, at 5:08 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Mohammad,
>
> You could use R.E.D. Server Dev./PyRED at
> http://q4md-forcefieldtools.org/REDServer-Development/
>
> PyRED generates force field for molecular fragments and does not only
> perform charge derivation.
>
> See http://q4md-forcefieldtools.org/REDServer-Development/news.php
> http://q4md-forcefieldtools.org/REDServer-Development/Documentation/
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
>
> Concerning a reasonable cocktail I would use a homogeneous system; For
> proteins and modified amino-acid residues I would simply use the last
> version of the Amber force field for... proteins.
>
> regards, Francois
>
>> I am working on a project involving a protein with an unnatural
>> fragment of the size of 3 amino acids (bonded to the rest of the
>> protein)
>>
>> I tried using ANTECHAMBER to do my fragment. I got the missing
>> interface parameters from the PARM99 file.
>> I later did the RED IV run. I just got the charges from that to
>> modify the files that I built with ANTECHAMBER.
>>
>> Now the simulation will include parameters as follows: For the
>> fragment, it got its atom types from GAFF (as made by antechamber)
>> and the charges from RED. The missing parameters I got from PARM99
>> and the rest of protein is dealt with regularly with, say, FF10SB.
>>
>> I am a newbie to dynamics, so I need an expert advice. Do you think
>> this is a reasonable cocktail? :)
>
>
>
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Received on Wed Sep 03 2014 - 15:30:02 PDT
