[gmx-users] [Fwd: Request]

[Alok]

Hello Yang,
                    Thanks for your Valuable suggestion.
  ----- Original Message ----- 
  From: Yang Ye 
  To: Discussion list for GROMACS users 
  Sent: Tuesday, June 14, 2005 3:16 PM
  Subject: Re: [gmx-users] [Fwd: Request]


  For question 1:

  You shall follow the second. And you shall have the definition as 

[ 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.
Regards,
  Yang Ye
  Computational Biology Lab
  School of Biological Sciences
  Nanyang Technological University
  Singapore
  Tel: 6316-2884



  David van der Spoel wrote: 
-------- 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

  

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