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.abra...@anu.edu.au
<mailto:mark.abra...@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
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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jalemkul[at]vt.edu | (540) 231-9080
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