[gmx-users] charge calculation........

[ABEL Stephane 175950]

Hi 

Since you want to use the AMBER force for your calculations, you will need to compute the RESP charges for your new residue (unprotoned TYR) and add the charges in your *rtp file. To compute the charges, you can use the RED.Server  (http://q4md-forcefieldtools.org/REDS/).

It is not easy, so read the tutorials.

HTH 

Stephane


----------------------

Dear All,

             I want to have one of tyrosine residues in my protein to
be unprotonated. I am using amber force field for the simulation. But
in aminoacid.rtp there is no entry for the unprotonated one. So I am
adding it by myself in to the .rtp file. Now I am bit confused with
the charge of the unprotonated one. How can I calculate the partial
charges for each and every atoms in  unprotonated tyrosine? Would
Gaussian/SCF be a good one to deal with this matter? Should I take the
tyrosine amino acid alone to calculate the charge in Gaussian ?
Please suggest me the proper method(s) to calculate the charge.

Thanks,

Tarak


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Message: 6
Date: Mon, 17 Sep 2012 08:08:22 -0400
From: Justin Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] visualize trajectory
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>,        Discussion list for
        GROMACS users <gmx-users at gromacs.org>
Message-ID: <505712B6.3030509 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



On 9/17/12 6:57 AM, Shima Arasteh wrote:
> Hi ,
>
> Which software is used to visualize a large mdrun output? For example 60 GB trajectory file.
>

I think you should probably have a look at
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume
before proceeding.  There are several programs that will work, provided you
don't exhaust the memory available on your workstation.

-Justin

--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================


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Message: 7
Date: Mon, 17 Sep 2012 08:10:27 -0400
From: Justin Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] Regarding RMSD graph nalysis
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <50571333.1060500 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



On 9/17/12 7:02 AM, naga sundar wrote:
> Dear gromacs users
>
> I run  20 ns MD simulation for protein mutant complexes. In RMSD analysis
> at ~9 ns sudden increase in the deviation was observed from 0.2 nm to 1.7
> nm and immediate fall was observed.
>
> I rerun the 20 ns simulation for the same molecule with same procedure.
> While analyzing the RMSD sudden increase in the deviation was observed (0.2
> nm to 1.7 nm) at the simulation period of ~12 ns.
>
> So i want to know  the reason
>
> For sudden rise and fall in RMSD values.
>
> Next, in first MD run this deviation was observed at ~9 ns (0.2 nm to 1.7
> nm) but while rerun the molecule with same procedure this deviation was
> observed at ~12 ns.
>

It sounds to me like your trajectories haven't correctly accounted for
periodicity.  g_rms does not elegantly handle sudden jumps across the box.  You
will need to work with trjconv.  Usually a simple trjconv -pbc mol -ur compact
-center does the trick for a simple protein, but for complexes it is often more
difficult.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

-Justin

--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================


------------------------------

Message: 8
Date: Mon, 17 Sep 2012 21:48:23 +0900
From: Rajiv Gandhi <grajiv03 at gmail.com>
Subject: Re: [gmx-users] Resuming of calculation from last *.cpt
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
        <CAPen9RXBKUf7MZJT8USbZreShWD9AMRiXh7XBp97OGtDZsBRAA at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Dear all,

I have read few papers regarding the photo dissociation event such
as Myoglobin heme-ligand bond deletion to induce the photodissociation in
MD simulation.

Could you please tell me the procedure how can i perform the
photodissociation mechanism in Gormacs and which force field have to use,

 Also I want to study Upon the photo dissociation their structural changes
in MD. Thanks in advance,



Regards

Rajiv


------------------------------

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