Re: [AMBER] How to calculate the parameters of metal ions?

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Thu, 31 Jul 2014 16:20:03 +0200

Dear Jingfeng Huang,

> I am simulating a protein with Co2+ at the active site. I have
> tried to search for the parameters that someone have released, but I
> found nothing. Herein, I hope you can provide me a strategy to
> solve the problem.

You could extract the active site with the metal (do not forget to
provide the hydrogen atoms), 'close' the open valencies if any. Indeed
a fragment does not exist in QM, and create a PDB file for this input
structure.

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

- provide the total charge & spin multiplicity values in the
Project.config file
See http://q4md-forcefieldtools.org/REDServer-Development/Documentation/
http://q4md-forcefieldtools.org/REDServer-Development/Documentation/Project.config
MOLECULE1-TOTCHARGE = your value
MOLECULE1-SPINMULT = your value

- provide the charge model & force field to be generated in the
System.config file
see
http://q4md-forcefieldtools.org/REDServer-Development/Documentation/System.config
set:
MOD_GAUSSIAN_JOB = Complex
CHR_TYP = RESP-X1
FFPARM = AMBERFF10

- create an archive file of the 3 files:
http://q4md-forcefieldtools.org/REDServer-Development/popup/poparchive.php
tar -jcvf archive Mol_red1.pdb Project.config System.config

- upload at:
http://q4md-forcefieldtools.org/REDServer-Development/upload-log.php

Misc:
. Do not forget to register and create a private account if you do
want to interface Gaussian:
See http://q4md-forcefieldtools.org/REDServer-Development/faq.php#3

. See the tutorial:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php

. See information about the mol3 force field library file format:
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php

I hope this helps,
regards, Francois



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Received on Thu Jul 31 2014 - 07:30:04 PDT