From 9b401b6ed0ab3e57763f1884ff461f0aea6f0994 Mon Sep 17 00:00:00 2001
From: Diego Ugarte <diego.ugarte@outlook.com>
Date: Tue, 20 Nov 2018 06:22:32 +0900
Subject: [PATCH 1/2] fix topology parsing

---
 tools/ch2lmp/charmm2lammps.pl | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tools/ch2lmp/charmm2lammps.pl b/tools/ch2lmp/charmm2lammps.pl
index 0693c0a0ff..df2a88fd30 100755
--- a/tools/ch2lmp/charmm2lammps.pl
+++ b/tools/ch2lmp/charmm2lammps.pl
@@ -794,9 +794,11 @@
         $ids{$tmp[1]}           = $tmp[2];
         $masses{$tmp[1]}        = $tmp[3];
         $max_id                 = $tmp[1] if ($max_id<$tmp[1]);
+      } elsif ($read&&($tmp[0] eq "ATOM")) {
+        # $names{$tmp[1]} = $tmp[4] if ($read&&($tmp[0] eq "MASS"));
+        #last if ($read&&!scalar(@tmp));                   # quit reading
+        last;
       }
-      # $names{$tmp[1]} = $tmp[4] if ($read&&($tmp[0] eq "MASS"));
-      last if ($read&&!scalar(@tmp));                   # quit reading
     }
     AddMass(HT, 1.00800);
     AddMass(OT, 15.99940);

From 6f7b052e24c819a1a3cdbfb96b84ea28ead9ad64 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 19 Nov 2018 16:38:25 -0500
Subject: [PATCH 2/2] update comments and remove commented code

---
 tools/ch2lmp/charmm2lammps.pl | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tools/ch2lmp/charmm2lammps.pl b/tools/ch2lmp/charmm2lammps.pl
index df2a88fd30..bda9ace2bc 100755
--- a/tools/ch2lmp/charmm2lammps.pl
+++ b/tools/ch2lmp/charmm2lammps.pl
@@ -795,8 +795,7 @@
         $masses{$tmp[1]}        = $tmp[3];
         $max_id                 = $tmp[1] if ($max_id<$tmp[1]);
       } elsif ($read&&($tmp[0] eq "ATOM")) {
-        # $names{$tmp[1]} = $tmp[4] if ($read&&($tmp[0] eq "MASS"));
-        #last if ($read&&!scalar(@tmp));                   # quit reading
+        # quit reading when hitting the "ATOM" section
         last;
       }
     }