add gromacs

bioexcel · Nov 21, 2024 · 322026a · 322026a
1 parent af70e0a
commit 322026a
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Showing 3 changed files with 3 additions and 1 deletion.
diff --git a/.github/env.yaml b/.github/env.yaml
@@ -7,6 +7,7 @@ dependencies:
   - biobb_common == 5.0.0
   - lipyphilic == 0.10.0
   - ambertools
+  - gromacs
   - hole2
   - pip:
     - fatslim
diff --git a/biobb_mem/fatslim/fatslim_membranes.py b/biobb_mem/fatslim/fatslim_membranes.py
@@ -102,7 +102,7 @@ def launch(self) -> int:
         self.tmp_cfg = str(PurePath(fu.create_unique_dir()).joinpath('output.gro'))
         self.cmd = ['gmx', 'editconf',
                     '-f', self.stage_io_dict["in"]["input_top_path"],
-                    '-o ', self.tmp_cfg,
+                    '-o', self.tmp_cfg,
                     '-box', ' '.join(map(str, u.dimensions[:3]))
                     ]
         self.tmp_out = str(PurePath(fu.create_unique_dir()).joinpath('output.ndx'))

diff --git a/biobb_mem/json_schemas/biobb_mem.json b/biobb_mem/json_schemas/biobb_mem.json
@@ -45,6 +45,7 @@
         "python >=3.9", 
         "biobb_common ==5.0.0",
         "ambertools >=22.0",
+        "gromacs",
         "lipyphilic ==0.10.0",
         "chap",
         "hole2",