Tons of small fixes to documentation.

[alexxy/gromacs.git] / src / kernel / pdb2gmx.c

diff --git a/src/kernel/pdb2gmx.c b/src/kernel/pdb2gmx.c
index 04895724d32ffb097a35ba80282822ed4bb9c7b2..8c8034a0a3079886131ed24de87fa2ffda4feb14 100644 (file)
--- a/src/kernel/pdb2gmx.c
+++ b/src/kernel/pdb2gmx.c
@@ -948,8 +948,8 @@ int main(int argc, char *argv[])
   const char *desc[] = {
     "This program reads a [TT].pdb[tt] (or [TT].gro[tt]) file, reads",
     "some database files, adds hydrogens to the molecules and generates",
-    "coordinates in Gromacs (Gromos), or optionally [TT].pdb[tt], format",
-    "and a topology in Gromacs format.",
+    "coordinates in GROMACS (GROMOS), or optionally [TT].pdb[tt], format",
+    "and a topology in GROMACS format.",
     "These files can subsequently be processed to generate a run input file.",
     "[PAR]",
     "[TT]pdb2gmx[tt] will search for force fields by looking for",
@@ -970,7 +970,7 @@ int main(int argc, char *argv[])
     "you will need to modify [TT]residuetypes.dat[tt] in the library directory",
     "or copy the whole library directory to a local directory and set",
     "the environment variable [TT]GMXLIB[tt] to the name of that directory.",
-    "Check chapter 5 of the manual for more information about file formats.",
+    "Check Chapter 5 of the manual for more information about file formats.",
     "[PAR]",
     
     "Note that a [TT].pdb[tt] file is nothing more than a file format, and it",
@@ -998,7 +998,7 @@ int main(int argc, char *argv[])
     "if you want a disulfide bridge or distance restraints between",
     "two protein chains or if you have a HEME group bound to a protein.",
     "In such cases multiple chains should be contained in a single",
-    "[TT]molecule_type[tt] definition.",
+    "[TT]moleculetype[tt] definition.",
     "To handle this, [TT]pdb2gmx[tt] has an option [TT]-chainsep[tt] so you can",
     "choose whether a new chain should start when we find a TER record,",
     "when the chain id changes, combinations of either or both of these",
@@ -1007,14 +1007,14 @@ int main(int argc, char *argv[])
     "[TT]pdb2gmx[tt] will also check the occupancy field of the [TT].pdb[tt] file.",
     "If any of the occupancies are not one, indicating that the atom is",
     "not resolved well in the structure, a warning message is issued.",
-    "When a [TT].pdb[tt] file does not originate from an X-Ray structure determination",
+    "When a [TT].pdb[tt] file does not originate from an X-ray structure determination",
     "all occupancy fields may be zero. Either way, it is up to the user",
     "to verify the correctness of the input data (read the article!).[PAR]", 
     
-    "During processing the atoms will be reordered according to Gromacs",
+    "During processing the atoms will be reordered according to GROMACS",
     "conventions. With [TT]-n[tt] an index file can be generated that",
     "contains one group reordered in the same way. This allows you to",
-    "convert a Gromos trajectory and coordinate file to Gromos. There is",
+    "convert a GROMOS trajectory and coordinate file to GROMOS. There is",
     "one limitation: reordering is done after the hydrogens are stripped",
     "from the input and before new hydrogens are added. This means that",
     "you should not use [TT]-ignh[tt].[PAR]",
@@ -1030,7 +1030,7 @@ int main(int argc, char *argv[])
     "position relative to neighboring atoms. Additionally, all atoms in the",
     "aromatic rings of the standard amino acids (i.e. PHE, TRP, TYR and HIS)",
     "can be converted into virtual sites, eliminating the fast improper dihedral",
-    "fluctuations in these rings. Note that in this case all other hydrogen",
+    "fluctuations in these rings. [BB]Note[bb] that in this case all other hydrogen",
     "atoms are also converted to virtual sites. The mass of all atoms that are",
     "converted into virtual sites, is added to the heavy atoms.[PAR]",
     "Also slowing down of dihedral motion can be done with [TT]-heavyh[tt]",
@@ -1157,24 +1157,24 @@ int main(int argc, char *argv[])
     { "-ter",    FALSE, etBOOL, {&bTerMan}, 
       "Interactive termini selection, iso charged" },
     { "-lys",    FALSE, etBOOL, {&bLysMan}, 
-      "Interactive Lysine selection, iso charged" },
+      "Interactive lysine selection, iso charged" },
     { "-arg",    FALSE, etBOOL, {&bArgMan}, 
-      "Interactive Arganine selection, iso charged" },
+      "Interactive arginine selection, iso charged" },
     { "-asp",    FALSE, etBOOL, {&bAspMan}, 
-      "Interactive Aspartic Acid selection, iso charged" },
+      "Interactive aspartic Acid selection, iso charged" },
     { "-glu",    FALSE, etBOOL, {&bGluMan}, 
-      "Interactive Glutamic Acid selection, iso charged" },
+      "Interactive glutamic Acid selection, iso charged" },
     { "-gln",    FALSE, etBOOL, {&bGlnMan}, 
-      "Interactive Glutamine selection, iso neutral" },
+      "Interactive glutamine selection, iso neutral" },
     { "-his",    FALSE, etBOOL, {&bHisMan},
-      "Interactive Histidine selection, iso checking H-bonds" },
+      "Interactive histidine selection, iso checking H-bonds" },
     { "-angle",  FALSE, etREAL, {&angle}, 
       "Minimum hydrogen-donor-acceptor angle for a H-bond (degrees)" },
     { "-dist",   FALSE, etREAL, {&distance},
       "Maximum donor-acceptor distance for a H-bond (nm)" },
     { "-una",    FALSE, etBOOL, {&bUnA}, 
-      "Select aromatic rings with united CH atoms on Phenylalanine, "
-      "Tryptophane and Tyrosine" },
+      "Select aromatic rings with united CH atoms on phenylalanine, "
+      "tryptophane and tyrosine" },
     { "-sort",   FALSE, etBOOL, {&bSort}, 
       "HIDDENSort the residues according to database, turning this off is dangerous as charge groups might be broken in parts" },
     { "-ignh",   FALSE, etBOOL, {&bRemoveH},