Re: [AMBER] nitro tyrosine

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Fri, 18 Mar 2016 13:03:12 +0100

Dear Wu Xu,

> I had a trouble in building prmtop and inpcrd files for nitro tyrosine.
> Therefore, I practiced to build tyrosine prmtop and inpcrd files.
> I generated nty.prepin (nty=new tyrosine) (attached), nty.frcmod
> (attached), and nty.lib (attached). However, new tyrosine is incorrect
> (nty.jpq, attached). G09 output file for tyrosine resp charge is attached
> too.

You could use PyRED at R.E.D. Server Dev.
http://q4md-forcefieldtools.org/REDServer-Development/

See tutorial:
http://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
  and
http://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#2

Then use:
http://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#16
and may be:
http://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#17
http://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#18

To generate the three fragments together:
http://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#25

To generate the three fragments automatically from a single input molecule:
http://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#26

Please note that the default format for FF libraries is the 'mol3'
file format:
see http://upjv.q4md-forcefieldtools.org/Tutorial/leap-mol3.php

regards, Francois


           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/


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Received on Fri Mar 18 2016 - 05:30:04 PDT