[gmx-users] [Fwd: Request]

[David van der Spoel]

-------- Forwarded Message --------
From: Alok <alokjain at iitk.ac.in>
To: spoel at xray.bmc.uu.se
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

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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