[gmx-users] Force field parameters for phosphorylated tyrosine
Justin A. Lemkul
jalemkul at vt.edu
Mon Jun 13 15:35:27 CEST 2011
bharat gupta wrote:
> thanks for the reply...
>
> Actually I have found the amber parameters for p-TYR from the following
> links : http://www.pharmacy.manchester.ac.uk/bryce/amber#pro
>
> I am not able to how build the residue topology .. shall I add the
> topology of phosphate only from this to normal tyrosine residue ??
>
You need to define a complete residue in an .rtp entry. See existing .rtp files
for examples and manual section 5.6.1.
-Justin
>
>
> !!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 <http://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
>
>
>
> On Mon, Jun 13, 2011 at 6:52 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
> On 13/06/2011 7:15 PM, bharat gupta wrote:
>
> Hi,
>
> Does gromacs and its associated FFs have parameters for
> phosphorylated tyrosine ??
>
>
> Probably not. The best place to search is the literature.
>
> Mark
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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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>
--
========================================
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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