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<tt>For question 1:<br>
<br>
You shall follow the second. And you shall have the definition as <br>
</tt>
<pre wrap=""><tt>[ molecules ]
; Compound #mols
Protein_A 1 (total 156 residues)
CA+ 2 (2 Ca ions)
SOL 151 (crystal water molecules present in PDB file)
Here, "molecules" section only indicate the composition and helps the assembly of the simulation system. It is not related to the actual effects of the ions. If you could define interaction between the ions and the protein, you can include ions in the itp and put the definition there. Leave the ions as ions and analyze the trajectory of them.
</tt></pre>
<div class="moz-signature"><i>Regards,</i><br>
Yang Ye<br>
<small><i>Computational Biology Lab<br>
School of Biological Sciences<br>
Nanyang Technological University<br>
Singapore<br>
Tel: 6316-2884<br>
</i></small>
</div>
<br>
<br>
David van der Spoel wrote:
<blockquote cite="mid1118741025.9127.36.camel@vangogh" type="cite">
<pre wrap="">-------- Forwarded Message --------
From: Alok <a class="moz-txt-link-rfc2396E"
href="mailto:alokjain@iitk.ac.in"><alokjain@iitk.ac.in></a>
To: <a class="moz-txt-link-abbreviated"
href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>
Subject: Request
Date: Tue, 14 Jun 2005 14:36:27 +0530 (IST)
hello david,
Sorry to bother with this personal mail.Actually i posted my
problem in the mailing list a couple of times but i did not
get any response and i am stuck with it.
I define the same problem as follows as I have done in
the gromacs mailing list.
********************************************
I have some doubts regarding simulation of my system with cofactors
and also about some suggestions on references of simulations on such systems.
First Question
##############
I have two Ca ions as a cofactor with my protein in the PDB file.
while using PDB2GMX, Should i define protein & cofactor (i.e. Ca) together
in the same
chain in the input PDB file or should i have to define different chain ID for
Protein &
Ca ions so as to distinguish them .
To be more clear on my problem, i define my PDB and topology file as below:
First: when i define protein and cofactor (Ca ions) in the same chain id
of the
input PDB file.
Eg: a section of my input PDB file
ATOM 1728 1HB CYS 118 25.225 110.035 -3.752 1.00 13.23
ATOM 1729 2HB CYS 118 24.087 108.787 -4.276 1.00 13.23
TER 1729 CYS 118
HETATM 1730 CA CA2+ 201 22.164 99.781 1.304 0.92 15.78
HETATM 1882 CA CA2+ 401 31.452 105.664 2.892 0.76 20.43
HETATM 1731 O HOH 202 20.707 99.706 3.256 0.89 16.45
HETATM 1732 O HOH 203 23.256 97.570 1.747 0.91 16.77
Eg: a section of the topology file.
[ molecules ]
; Compound #mols
Protein 1 (total 118 Protein Residues +2 Ca =120 residues)
SOL 151 (crystal water molecules present in PDB file)
Second: WHen i define protein and cofactor (Ca ions) in different chain id
of the
input PDB file.
Eg: a section of my input PDB file
ATOM 1726 H CYS A 118 26.489 111.329 -5.466 1.00 9.69
ATOM 1727 HA CYS A 118 25.013 108.997 -6.671 1.00 11.08
ATOM 1728 1HB CYS A 118 25.225 110.035 -3.752 1.00 13.23
ATOM 1729 2HB CYS A 118 24.087 108.787 -4.276 1.00 13.23
TER 1729 CYS A 118
HETATM 1730 CA CA2+ B 201 22.164 99.781 1.304 0.92 15.78
HETATM 1882 CA CA2+ B 401 31.452 105.664 2.892 0.76 20.43
HETATM 1731 O HOH 202 20.707 99.706 3.256 0.89 16.45
HETATM 1732 O HOH 203 23.256 97.570 1.747 0.91 16.77
Eg: A section of the topology file.
[ molecules ]
; Compound #mols
Protein_A 1 (total 156 residues)
Protein_B 1 (2 Ca ions)
SOL 151 (crystal water molecules present in PDB file)
So which of these two options should i follow in defining my system???
Second Question
###############
Also I would like to know if there are any reported simulation of a
system in which
Ca/Mg/Zn ions are present
as cofactors.
I would be extremely thankfull if anyone could could suggest me any
reference(s) of
papers published on simulations
of system with these ions as cofactors.
Actually I am little apprehensive about the force field parameters of
these ions as
i have not come accross papers
on simulation with these ions present..
please guide me to overcome these situations.
Thanks in Advance.
Sorry to bother you personally on this.
Alok Jain
</pre>
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