Re: [AMBER] query

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Tue, 07 Apr 2015 08:09:21 +0200

Hi,

> We have a protein which contain Iron (Fe2+, co-ordinated to Cys, His,
> His) and we are simulating this protein along with iron according to
> "AMBER TUTORIAL A1". Can you please tell us how to create a frcmod file
> with the changes specific to this project. Do we need to use some
> software, if so then please specify.

See http://ambermd.org/formats.html
http://q4md-forcefieldtools.org/REDServer-Development/RED-Server-demo1.php
  & its test case:
http://q4md-forcefieldtools.org/REDServer-Development/popup/poptestcase.php
  and frcmod file:
http://q4md-forcefieldtools.org/REDServer-Development/Demo2-Files/frcmod.user

You could use PyRED at R.E.D. Server Dev. at
http://q4md-forcefieldtools.org/REDServer-Development/
   frcmod files, LEaP script and force field libraries are generated
from the PDB input files...

See tutorials: http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
   and in particular
        http://q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo1.pdf
        http://q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo21.pdf

regards, Francois




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Received on Mon Apr 06 2015 - 23:30:02 PDT