Re: [AMBER] Building parameter files for a zinc finger

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Sat, 11 Jan 2014 14:01:13 +0100

Dear Yip Yew Mun,

> I'm currently planning to simulate a zinc finger where 4 cysteine
> residues are coordinated to a zinc ion. I changed the CYS to CYM. I
> also created a non-standard residue for the zinc ion. I wish to ask
> if I need to explicitly use the command "bond" to bond the SG atom
> of my CYM residues to the zinc ion.?

If you decide to use R.E.D. Server Dev. provide a PDB input for the
active site (no need to define the bonds if the geometry given as
input is reasonable); R.E.D. Python will generate the FF for you and
list missing FF parameters if any.

4 cys(-) + Zn2+ -> total charge : -2

Zn 30 (12) [Ar].3d10.4s2 || || || || || ||
Zn++ [Ar].3d10 || || || || ||
     -> spin multiplicity 1

Provide a Project.config file with only
MOLECULE1-TOTCHARGE = -2
See
http://q4md-forcefieldtools.org/REDS-Development/Demo2-Files/Project.config

Provide a configurtion.py file with only
CHR_TYP = "RESP-X1"
MOD_GAUSSIAN_JOB = "complex"
See
http://q4md-forcefieldtools.org/REDS-Development/Demo2-Files/Configuration.py

tar zcvf Archive.tgz Mol_red1.pdb Project.config Configuration.py
see http://q4md-forcefieldtools.org/REDS-Development/popup/poparchive.php

& upload this archive file at
http://q4md-forcefieldtools.org/REDS-Development/upload-log.php
(after registration: see
http://q4md-forcefieldtools.org/REDS-Development/faq.php#3 to get a
private account)

then we will discuss about the data generated:
See http://q4md-forcefieldtools.org/REDS-Development/faq.php#5

regards, Francois



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Received on Sat Jan 11 2014 - 05:30:02 PST