[gmx-users] Re: gmx-users Digest, Vol 104, Issue 73
fatemeh ramezani
fr_750 at yahoo.com
Mon Dec 17 22:01:25 CET 2012
Dear Justin
According to papers, I expect gold atom interacts with the sulfur atom of amino acid cysteine covalently. But in last email you said in the case of protein-Au This will not be true to add these parameters
in topology file. Then in which file should I add the parameters between gold and sulfur?
What do you suggest? How do I define for the program that can be established between these two atoms covalent bond ?
many thanks
Fatemeh Ramezani
________________________________
From: "gmx-users-request at gromacs.org" <gmx-users-request at gromacs.org>
To: gmx-users at gromacs.org
Sent: Monday, 17 December 2012, 1:47
Subject: gmx-users Digest, Vol 104, Issue 73
Send gmx-users mailing list submissions to
gmx-users at gromacs.org
To subscribe or unsubscribe via the World Wide Web, visit
http://lists.gromacs.org/mailman/listinfo/gmx-users
or, via email, send a message with subject or body 'help' to
gmx-users-request at gromacs.org
You can reach the person managing the list at
gmx-users-owner at gromacs.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."
Today's Topics:
1. Re: Parametrisation of the cyclic nucleotides in Gromos force
fields (James Starlight)
2. Re: Parametrisation of the cyclic nucleotides in Gromos force
fields (Justin Lemkul)
3. Re: gold-S simulation (fatemeh ramezani)
4. Re: gold-S simulation (fatemeh ramezani)
5. Re: gold-S simulation (francesco oteri)
6. Box Pressure on individual box walls (John Doe)
7. Re: Box Pressure on individual box walls (David van der Spoel)
8. Re: gold-S simulation (Justin Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Sun, 16 Dec 2012 19:34:57 +0400
From: James Starlight <jmsstarlight at gmail.com>
Subject: Re: [gmx-users] Parametrisation of the cyclic nucleotides in
Gromos force fields
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<CAALQopzp6xCweeYWRcmMsZNYDnEvg_=gjPqOfRLaZpHv5dduPQ at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Justin, thanks again for explanation.
So the first 5 atoms in cmap.it correspond to the starting sequence of
the backbone atoms of the amino acid doesnt it ? So what is the 24 24
numbers at the end of each cmap line ?
E.g in the C NH1 CT1 C NC=O 1 24 24\ the first C B CA C N atoms would
be assigned as the backbone. That lines were added after grompp
produce error about unknown cmap for that 5 atoms of the chromophore.
Should the 24 24 \ be removed from each line of the chromophore cmap ?
James
------------------------------
Message: 2
Date: Sun, 16 Dec 2012 11:12:35 -0500
From: Justin Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] Parametrisation of the cyclic nucleotides in
Gromos force fields
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <50CDF2F3.4030703 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 12/16/12 10:34 AM, James Starlight wrote:
> Justin, thanks again for explanation.
> So the first 5 atoms in cmap.it correspond to the starting sequence of
> the backbone atoms of the amino acid doesnt it ? So what is the 24 24
> numbers at the end of each cmap line ?
Probably something related to how Gromacs tools read in the CMAP data. I don't
have time to go through the code to find exactly how it's used.
> E.g in the C NH1 CT1 C NC=O 1 24 24\ the first C B CA C N atoms would
> be assigned as the backbone. That lines were added after grompp
> produce error about unknown cmap for that 5 atoms of the chromophore.
> Should the 24 24 \ be removed from each line of the chromophore cmap ?
>
You shouldn't be modifying anything about cmap.itp, nor should those numbers be
present in your .rtp file. Your [cmap] directive in the .rtp entry should
contain a sequence of 5 atom names to which the CMAP corrections are applied.
-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: 3
Date: Sun, 16 Dec 2012 09:58:16 -0800 (PST)
From: fatemeh ramezani <fr_750 at yahoo.com>
Subject: Re: [gmx-users] gold-S simulation
To: "gmx-users-request at gromacs.org" <gmx-users-request at gromacs.org>,
"gmx-users at gromacs.org" <gmx-users at gromacs.org>,
"gmx-users-owner at gromacs.org" <gmx-users-owner at gromacs.org>
Message-ID:
<1355680696.17757.YahooMailNeo at web113504.mail.gq1.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1
Dear francesco
I extract gold parameter from papers that I attached them for you. But for gold and other atom parameters, you should calculate them using common combination rule.
Fatemeh Ramezani
________________________________
------------------------------
Message: 4
Date: Sun, 16 Dec 2012 10:00:03 -0800 (PST)
From: fatemeh ramezani <fr_750 at yahoo.com>
Subject: Re: [gmx-users] gold-S simulation
To: "gmx-users-request at gromacs.org" <gmx-users-request at gromacs.org>,
"gmx-users at gromacs.org" <gmx-users at gromacs.org>,
"gmx-users-owner at gromacs.org" <gmx-users-owner at gromacs.org>
Message-ID:
<1355680803.57169.YahooMailNeo at web113507.mail.gq1.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1
hi
thanks for your attention,
all itp files are in OPLSAA forcefield folder that I attached it for you.
Fatemeh Ramezani
________________________________
------------------------------
Message: 5
Date: Sun, 16 Dec 2012 19:11:14 +0100
From: francesco oteri <francesco.oteri at gmail.com>
Subject: Re: [gmx-users] gold-S simulation
To: fatemeh ramezani <fr_750 at yahoo.com>, Discussion list for GROMACS
users <gmx-users at gromacs.org>
Cc: "gmx-users-owner at gromacs.org" <gmx-users-owner at gromacs.org>,
"gmx-users-request at gromacs.org" <gmx-users-request at gromacs.org>
Message-ID:
<CAFQcp-OLnQncY2fUdfEiXEff9Ao4DmgAONnUfi1gasx1e4_mpg at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi fatemeh,
thank you for the references. Regarding your problem, what does it means
you don't see any interaction?
Is it possible it is just a problem of the visualization software. To be
sure, you could monitor the distance
between any S atom and the Au atom to which it is supposed to be bound. If
the distance is stable around
the equilibrium value you can say that the interaction is still present
Francesco
2012/12/16 fatemeh ramezani <fr_750 at yahoo.com>
>
>
> hi
> thanks for your attention,
> all itp files are in OPLSAA forcefield folder that I attached it for you.
>
>
>
> Fatemeh Ramezani
>
>
> ________________________________
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
Cordiali saluti, Dr.Oteri Francesco
------------------------------
Message: 6
Date: Sun, 16 Dec 2012 20:09:07 +0000
From: John Doe <helstreak at hotmail.com>
Subject: [gmx-users] Box Pressure on individual box walls
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Message-ID: <BLU169-W126DF4BBA792E2B92D3E7A8B4330 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
Hello All,
I was wondering if it's possible to get the pressure on individual walls of a pbc cubic box. I specifically want the pressure on the walls perpendicular to the x, y, z axis.
Thank you for your time.
------------------------------
Message: 7
Date: Sun, 16 Dec 2012 21:45:47 +0100
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] Box Pressure on individual box walls
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <50CE32FB.9050208 at xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2012-12-16 21:09, John Doe wrote:
>
> Hello All,
>
> I was wondering if it's possible to get the pressure on individual walls of a pbc cubic box. I specifically want the pressure on the walls perpendicular to the x, y, z axis.
>
g_energy will do it.
> Thank you for your time.
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
------------------------------
Message: 8
Date: Sun, 16 Dec 2012 17:15:56 -0500
From: Justin Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] gold-S simulation
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <50CE481C.2020703 at vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed
On 12/16/12 1:11 PM, francesco oteri wrote:
> Hi fatemeh,
> thank you for the references. Regarding your problem, what does it means
> you don't see any interaction?
> Is it possible it is just a problem of the visualization software. To be
> sure, you could monitor the distance
> between any S atom and the Au atom to which it is supposed to be bound. If
> the distance is stable around
> the equilibrium value you can say that the interaction is still present
>
In addition, if one is expecting some sort of covalent association, it must be
defined in the topology. This will not be true in the case of protein-Au
interactions unless one makes appropriate entries in specbond.dat, similar to
heme, or manual addition. Bonded parameters are useless unless there is a bond :)
-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
========================================
------------------------------
--
gmx-users mailing list
gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
End of gmx-users Digest, Vol 104, Issue 73
******************************************
More information about the gromacs.org_gmx-users
mailing list