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 Sat Aug 30 2014 - 04:30:02 PDT
