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--- > 1 > 7 6 5 1 HG 2007/5/24, j j <fantvamp.gmail.com>: > > Dear Amber User, > I'm trying to add polar Hydrogens by using protonate by doing: > protonate -d PROTON_INFO.kollua_polH < prot_in.pdb > prot_out_polH.pdb > When I check results I think HG is missing in CYS residues: > charge CYS_prot_out_polH.pdbq > ATOM 101 N CYS B 12 -13.623 -0.254 8.103 0.00 0.00 - > 0.520 > ATOM 102 HN CYS B 12 -14.244 0.084 7.382 0.00 0.00 > 0.248 > ATOM 103 CA CYS B 12 - 12.630 -1.259 7.786 0.00 0.00 > 0.146 > ATOM 104 C CYS B 12 -11.306 -0.844 8.366 0.00 0.00 > 0.526 > ATOM 105 O CYS B 12 -10.816 -1.447 9.314 0.00 0.00 - > 0.500 > ATOM 106 CB CYS B 12 - 12.475 -1.416 6.290 0.00 0.00 > 0.100 > ATOM 107 SG CYS B 12 -11.079 -2.451 5.880 0.00 0.00 - > 0.135 > Total Charge -0.1350 in CYS_prot_out_polH.pdbq > I expected to have: > charge CYS > q[ "CYS", "N" ] = -0.5200 > q[ "CYS", "CA" ] = 0.1460 > q[ "CYS", "HN" ] = 0.2480 > q[ "CYS", "C" ] = 0.5260 > q[ "CYS", "O" ] = -0.5000 > q[ "CYS", "CB" ] = 0.1000 > q[ "CYS", "SG" ] = -0.1350 > q[ "CYS", "HG" ] = 0.1350 > Total Charge 0.0000 in CYS > as especified in the q.kollua.amber > To do this I though in modifying the PROTON_INFO.kollua_polH by adding: > 29,30c29,30 > < CYS 6 > < CA N C O CB SG > --- > > CYS 7 > > CA N C O CB SG HG > As specified in the protonate.f: > c*****add all protons to a protein structure according to formulae > c*****specified in a PROTON_INFO file. > I'm missing again the HG so do not seem to work. > I saw this message about it in the reflector, > so I'm writting. > Thank you, > JJ > > > 2006/10/11, Sean Rathlef < sean.syncitium.net>: > > > > I'm trying to add polar hydrogens to a PDB file using PROTONATE.exe(oringinally from autodock, I think). I tried the command lines with the > > executable, but could not generate the desired output PDB file. If > > anyone knows the proper command line calls (perhaps an example), please > > advise. > > > > I tried the following: > > protonate.exe < name.pdb > out.pdb > > > > which generated: > > PROTON_INFO, protonate.exe.stackdump, and out.pdb > > > > The only file with anything in it was the stackdump > > Stack trace: > > Frame Function Args > > End of stack trace > > > > Do I need to use PROTON_INFO.kollua_polH, as in: > > protonate.exe -k PROTON_INFO.kollua_polH < name.pdb > out.pdb > > > > Because I tried that, also with the "-d" flag an that didn't work > > either. > > > > Help greatly appreciated. > > Sean > > > > > > > > -- > fantvamp ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Sun May 27 2007 - 06:07:24 PDT