[gmx-users] Umbrella sampling of phosphate ion binding
Dallas Warren
Dallas.Warren at monash.edu
Thu Jun 9 03:30:34 CEST 2011
You have been provided there with the reference in which the parameters for the molecule were derived.
Read it!
And determine yourself if it is applicable or not to what you are doing and the forcefield you are using.
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of bharat gupta
Sent: Thursday, 9 June 2011 11:29 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Umbrella sampling of phosphate ion binding
I found it in the /shared/top/ gmx.ff folder . Here's the file
;
; Force field based on GROMOS with new charges as described in
; D. van der Spoel, K.A. Feenstra, M.A. Hemminga and H.J.C. Berendsen:
; Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic
; mottle virus coat protein in solution with phosphate ions
; Biophys. J. 71 pp. 2920-2932 (1996)
;
[ moleculetype ]
; name nrexcl
h2po4 4
[ atoms ]
; nr type resnr residu atom cgnr charge mass
; use charges from Janez Mavri
1 OA 1 PI O1 1 -0.777
2 OA 1 PI O2 1 -0.777
3 OM 1 PI O3 1 -0.943
4 OM 1 PI O4 1 -0.943
5 P 1 PI P 1 1.596
6 HO 1 PI H1 1 0.422
7 HO 1 PI H2 1 0.422
[ bonds ]
; ai aj funct c0 c1
5 1 1 1.637000e-01
5 2 1 1.637000e-01
5 3 1 1.478000e-01
5 4 1 1.478000e-01
6 1 1 0.943000e-01
7 2 1 0.943000e-01
[ angles ]
; ai aj ak funct c0 c1
2 5 1 1 1.015000e+02 400
3 5 1 1 1.059000e+02
4 5 1 1 1.082000e+02
3 5 2 1 1.059000e+02
4 5 2 1 1.082000e+02
4 5 3 1 1.248000e+02
6 1 5 1 1.082000e+02
7 2 5 1 1.082000e+02
[ dihedrals ]
; ai aj ak al funct
6 1 5 2 1
7 2 5 1 1
Can I use it or not ??
On Thu, Jun 9, 2011 at 10:26 AM, Justin A. Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:
bharat gupta wrote:
does the gromacs force field has topology and ff parameter for H2PO4(-) ion . As I have derived both topology and FF parameter from prodrug
Probably not; check the .rtp file for your desired force field.
server and after checking the topology I found that it has deleted of the hydrogen.
See the PRODRG FAQ; this gets asked all the time.
http://davapc1.bioch.dundee.ac.uk/prodrg/prodrg_faq.html
No matter what PRODRG gives you, the charges will probably be useless anyway:
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
So you're in for the difficult process of parameterization if no one's already developed parameters for your molecule:
http://www.gromacs.org/Documentation/How-tos/Parameterization
-Justin
On Thu, Jun 9, 2011 at 10:16 AM, Justin A. Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu<mailto:jalemkul at vt.edu>>> wrote:
bharat gupta wrote:
Hi Justin,
I am having following doubts regarding umbrella sampling of
phosphate ion binding to my protein .
1. As per the tutorial, I need to fix an immobile reference. In
my case which region do I have to fix as my protein consists of
one single chain. Since I am studying the binding and unbinding
of ion, shall I fix the ion fixed. If it's so, then do I have to
give a different chain name for it as my complex doesnot chain
name for ion/ligand.
You don't need an immobile reference just because my tutorial did.
I had a particular need to do so. For your purpose, I highly doubt
it's necessary. You're looking at small molecule-protein
interactions, not protein-protein interactions.
2. What should be the size of box and how do I know where to
place the protein's COM in box (the precise location).
The absolute COM is somewhat irrelevant; all distances during
pulling are relative. You can place the protein in a certain
location in the box for convenience if you like. The box size must
be greater than twice the pull distance, as explained in the
tutorial. The amount that you wish to pull will dictate both the
location of the protein and the box size.
-Justin
-- ==============================__==========
Justin A. Lemkul
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Bharat
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com<mailto:monu46010 at yahoo.com>
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