.TH PROTONATE L "10 August 1992".SH NAMEprotonate \- add protons to a heavy-atom protein or DNA PDB file; convertproton names between various conventions; check (pro)-chirality.SH SYNOPSIS.B protonate[ -k ] [ -b ] [ -d info-file ] <.I input-pdb-file>.I protonated-pdb-file.SH DESCRIPTION.I Protonatecombines a program originally written by K. Cross to add protons to aheavy-atom pdb file with many extensions by G.P. Gippert & D.A.Case.  Names anddescriptions of the output protons are contained in the info-file (seebelow.)  \fIProtonate\fR can be used to add protons that don't exist, tochange the names of existing protons to some new convention, and tocheck pro-chirality of protons in an input pdb file.  If the .I -kflag is specified, the output pdb file will "keep" the protoncoordinates of the input file, to the extent consistent with how wellit can identify what names they should "really" have.  Otherwise itwill replace input protons with ones it builds.  If the .I -bflag is set, the program will add a space to the beginning of eachheavy atom as it writes it to the output file.  This is most oftenusedto convert input files whose atom names begin in column 13 to theBrookhaven format where most heavy atom names begin in column 14.NOTE: "two-letter" heavy atom names (like FE or CA [calcium]) willnot be correct; the resulting output file must be hand-edited to checkfor this..SH FILES.HP.I PROTON_INFOis the default name for information on how to build andname protons, and isused to determine where on the amino acids the protons should beplaced.  This file currently knows about funny amber residue nameslike HIE, HIP and HID and HEM.  The location of this file can bespecified by the .I -dflag.  Currently, our working version resides in /frege/mm/protonate..HPOther files provided include PROTON_INFO.Brook, which uses Brookhavenproton naming convention (things like 1HB, etc.), andPROTON_INFO.oldnames, which uses "old" amber names.  Use the -d flagto indicate the name of the file whose names you want in the output.For example, to take an amber pdb file and convert to the Brookhavennaming convention, set "-d PROTON_INFO.Brook"..HPOutput to STDERR includes "matches" of protons the program buildswith any found in the input file, plus a list of any input protonsthat could not be matched.  Questionable "matches" are flagged andshould be checked manually..SH BUGS.HPFormat of the PROTON_INFO file is not obvious unless you have readthe code..HPMethyl protons are built in a staggered conformation; hydroxyl protonsin a arbitrary (and generally sub-optimal) conformation.  A programlike "pol_h" or its equivalent should be used (if desired) toplace polar hydrogens on LYS, SER, THR, and SER residues..HPHIS in input file is assumed to be HID.  Users should generallyexplicitly figure out the desired protonation state for histidines..HPDoesn't even try to identify heavy atoms in the input file that havetwo-letter element names; this means that "Brookhaven"-style outputmay require some hand-editing if atoms like calcium or iron arepresent..HPAssumes that the "alternate conformer" flag in column 17 of the PDB fileshould be either blank, or "A".  The program needs to be recompiled tochange this; perhaps this should become an input option.