From 3484d3a72d2cf3954c7115a0eeeecde167855970 Mon Sep 17 00:00:00 2001
From: amjjbonvin <alexandre.bonvin@gmail.com>
Date: Wed, 13 Apr 2022 10:45:23 +0200
Subject: [PATCH] Solves issue #400

---
 examples/scoring/mdscoring-test.cfg                    |  1 +
 .../modules/scoring/mdscoring/cns/mdscoring.cns        | 10 +++++++++-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/examples/scoring/mdscoring-test.cfg b/examples/scoring/mdscoring-test.cfg
index e23a16f17..3f5da8ca6 100644
--- a/examples/scoring/mdscoring-test.cfg
+++ b/examples/scoring/mdscoring-test.cfg
@@ -23,5 +23,6 @@ tolerance = 20
 contactairs = true
 ssdihed = "alphabeta"
 dnarest_on = true
+#keepwater = true
 
 # ====================================================================
diff --git a/src/haddock/modules/scoring/mdscoring/cns/mdscoring.cns b/src/haddock/modules/scoring/mdscoring/cns/mdscoring.cns
index 32e32c78f..9bbd10861 100644
--- a/src/haddock/modules/scoring/mdscoring/cns/mdscoring.cns
+++ b/src/haddock/modules/scoring/mdscoring/cns/mdscoring.cns
@@ -423,10 +423,18 @@ inline @MODULE:print_coorheader.cns
 
 coor sele= (not name H* and not resn ANI and not resn XAN and not resn DAN) orient end
 
-write coordinates format=pdbo output=$output_pdb_filename end
+write coordinates sele=(not (resn WA* or resn HOH or resn TIP* or resn DMS)) format=pdbo output=$output_pdb_filename end
 
 set message=normal echo=on end
 
 display OUTPUT: $output_pdb_filename
 
+if ($refine.keepwater eq true) then
+    evaluate ($filename= $output_pdb_filename - ".pdb" + "_solvent.pdb")
+    write coordinates sele=(all) format=pdbo output=$filename end
+end if
+
+display OUTPUT: $output_pdb_filename
+
 stop
+