[gmx-users] Umbrella sampling of phosphate ion binding
bharat gupta
bharat.85.monu at gmail.com
Thu Jun 9 06:52:01 CEST 2011
Hi,
After searching I have found parameters for phosphorylated tyrosine. And my
experiment also involves that as in this case phosphate ion only binds to
the active site. So, can I use the parameter for umbrella sampling taken
from amber parameter database.
!!index array str
"Y1P"
!entry.Y1P.unit.atoms table str name str type int typex int resx
int flags int seq int elmnt dbl chg
"N" "N" 0 1 131073 1 7 -0.516300
"H" "H" 0 1 131073 2 1 0.293600
"CA" "CT" 0 1 131073 3 6 0.275503
"HA" "H1" 0 1 131073 4 1 0.008223
"CB" "CT" 0 1 131073 5 6 -0.354052
"HB2" "HC" 0 1 131073 6 1 0.110326
"HB3" "HC" 0 1 131073 7 1 0.110326
"CG" "CA" 0 1 131073 8 6 0.119728
"CD1" "CA" 0 1 131073 9 6 -0.198938
"HD1" "HA" 0 1 131073 10 1 0.137143
"CE1" "CA" 0 1 131073 11 6 -0.284884
"HE1" "HA" 0 1 131073 12 1 0.177179
"CZ" "C" 0 1 131073 13 6 0.452616
"CE2" "CA" 0 1 131073 14 6 -0.284884
"HE2" "HA" 0 1 131073 15 1 0.177179
"CD2" "CA" 0 1 131073 16 6 -0.198938
"HD2" "HA" 0 1 131073 17 1 0.137143
"OG" "OS" 0 1 131073 18 8 -0.534452
"P" "P" 0 1 131073 19 15 1.393213
"O1P" "OH" 0 1 131073 20 8 -0.752821
"O2P" "O2" 0 1 131073 21 8 -0.822464
"O3P" "O2" 0 1 131073 22 8 -0.822464
"H1P" "HO" 0 1 131073 23 1 0.423316
"C" "C" 0 1 131073 24 6 0.536600
"O" "O" 0 1 131073 25 8 -0.581900
!entry.Y1P.unit.atomspertinfo table str pname str ptype int ptypex
int pelmnt dbl pchg
"N" "N" 0 -1 0.0
"H" "H" 0 -1 0.0
"CA" "CT" 0 -1 0.0
"HA" "H1" 0 -1 0.0
"CB" "CT" 0 -1 0.0
"HB2" "HC" 0 -1 0.0
"HB3" "HC" 0 -1 0.0
"CG" "CA" 0 -1 0.0
"CD1" "CA" 0 -1 0.0
"HD1" "HA" 0 -1 0.0
"CE1" "CA" 0 -1 0.0
"HE1" "HA" 0 -1 0.0
"CZ" "C" 0 -1 0.0
"CE2" "CA" 0 -1 0.0
"HE2" "HA" 0 -1 0.0
"CD2" "CA" 0 -1 0.0
"HD2" "HA" 0 -1 0.0
"OG" "OS" 0 -1 0.0
"P" "P" 0 -1 0.0
"O1P" "OH" 0 -1 0.0
"O2P" "O2" 0 -1 0.0
"O3P" "O2" 0 -1 0.0
"H1P" "HO" 0 -1 0.0
"C" "C" 0 -1 0.0
"O" "O" 0 -1 0.0
!entry.Y1P.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.Y1P.unit.childsequence single int
2
!entry.Y1P.unit.connect array int
1
24
!entry.Y1P.unit.connectivity table int atom1x int atom2x int flags
1 2 17
1 3 17
3 4 17
3 24 17
3 5 17
5 6 17
5 7 17
5 8 17
8 16 17
8 9 17
9 10 17
9 11 17
11 12 17
11 13 17
13 18 17
13 14 17
14 15 17
14 16 17
16 17 17
18 19 17
19 22 17
19 21 17
19 20 17
20 23 17
24 25 17
!entry.Y1P.unit.hierarchy table str abovetype int abovex str
belowtype int belowx
"U" 0 "R" 1
"R" 1 "A" 1
"R" 1 "A" 2
"R" 1 "A" 3
"R" 1 "A" 4
"R" 1 "A" 5
"R" 1 "A" 6
"R" 1 "A" 7
"R" 1 "A" 8
"R" 1 "A" 9
"R" 1 "A" 10
"R" 1 "A" 11
"R" 1 "A" 12
"R" 1 "A" 13
"R" 1 "A" 14
"R" 1 "A" 15
"R" 1 "A" 16
"R" 1 "A" 17
"R" 1 "A" 18
"R" 1 "A" 19
"R" 1 "A" 20
"R" 1 "A" 21
"R" 1 "A" 22
"R" 1 "A" 23
"R" 1 "A" 24
"R" 1 "A" 25
!entry.Y1P.unit.name single str
"Y1P"
!entry.Y1P.unit.positions table dbl x dbl y dbl z
-2.803000 1.247000 -0.295000
-1.865000 1.556000 -0.174000
-3.015000 0.022000 -1.037000
-3.856000 0.168000 -1.700000
-1.782000 -0.305000 -1.915000
-1.962000 -1.275000 -2.366000
-1.774000 0.418000 -2.724000
-0.435000 -0.281000 -1.219000
0.338000 0.878000 -1.203000
-0.007000 1.752000 -1.735000
1.552000 0.940000 -0.541000
2.153000 1.829000 -0.549000
2.035000 -0.183000 0.121000
1.299000 -1.362000 0.075000
1.704000 -2.235000 0.553000
0.083000 -1.405000 -0.581000
-0.466000 -2.331000 -0.607000
3.171000 -0.146000 0.830000
4.653000 0.133000 0.090000
5.550000 -0.029000 1.430000
4.676000 1.556000 -0.300000
4.905000 -0.981000 -0.825000
5.675000 0.835000 1.798000
-3.448000 -1.169000 -0.177000
-4.236000 -1.966000 -0.612000
!entry.Y1P.unit.residueconnect table int c1x int c2x int c3x int
c4x int c5x int c6x
1 24 0 0 0 0
!entry.Y1P.unit.residues table str name int seq int childseq int
startatomx str restype int imagingx
"Y1P" 1 26 1 "p" 0
!entry.Y1P.unit.residuesPdbSequenceNumber array int
1
!entry.Y1P.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.Y1P.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
# Parameters for TYR-PO2(OH) : Y1P; N.Homeyer, A.H.C.Horn, H.Lanig,
H.Sticht, J. Mol. Model., in press
BOND
OS - P 525.0 1.610
OH - P 525.0 1.610
ANGLE
C - OS - P 100.0 120.50
O2 - P - OH 140.0 108.23
HO - OH - P 140.0 108.50
CA - C - OS 70.0 120.00
DIHE
IMPR
CA-CA-C-OS 1.1 180.0 2.0
Now, can this be used ...
On Thu, Jun 9, 2011 at 10:30 AM, Dallas Warren <Dallas.Warren at monash.edu>wrote:
> 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> 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>> 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
> 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
> <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
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>
> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>****
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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>
> --
> 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****
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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
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