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.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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- 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 : monu46...@yahoo.com
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
