[gmx-users] Force field parameters for phosphorylated tyrosine
bharat gupta
bharat.85.monu at gmail.com
Mon Jun 13 15:33:15 CEST 2011
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 ??
!!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
On Mon, Jun 13, 2011 at 6:52 PM, Mark Abraham <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
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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