add docs for user defined amber masks #454

Valdes-Tresanco-MS · Jan 18, 2024 · a8a326d · a8a326d
1 parent f745330
commit a8a326d
Show file tree

Hide file tree

Showing 2 changed files with 46 additions and 24 deletions.
diff --git a/docs/examples/QM_MMGBSA/README.md b/docs/examples/QM_MMGBSA/README.md
@@ -17,16 +17,16 @@ title: QM/MMGBSA
 
 In this case, `gmx_MMPBSA` requires:
 
-| Input File required            | Required |           Type             | Description |
-|:-------------------------------|:--------:|:--------------------------:|:-------------------------------------------------------------------------------------------------------------|
-| Input parameters file          | :octicons-check-circle-fill-16:{ .req .scale_icon_medium } |           `in`          | Input file containing all the specifications regarding the type of calculation that is going to be performed |
-| The MD Structure+mass(db) file | :octicons-check-circle-fill-16:{ .req .scale_icon_medium } |    `tpr` `pdb`    | Structure file containing the system coordinates |
-| An index file                  | :octicons-check-circle-fill-16:{ .req .scale_icon_medium } |          `ndx`    | File containing the receptor and ligand in separated groups |
-| Receptor and ligand group      | :octicons-check-circle-fill-16:{ .req .scale_icon_medium } |        `integers`       | Group numbers in the index files |
-| A trajectory file              | :octicons-check-circle-fill-16:{ .req .scale_icon_medium } | `xtc` `pdb` `trr` | Final GROMACS MD trajectory, fitted and with no pbc. |
-| Ligand parameters file         | :octicons-check-circle-fill-16:{ .req .scale_icon_medium } |          `mol2`         | The Antechamber output  `mol2` file of ligand parametrization|
-| A topology file (not included) | :octicons-check-circle-fill-16:{ .req_opt .scale_icon_medium }    |           `top`         | GROMACS topology file (The `* .itp` files defined in the topology must be in the same folder |
-| A Reference Structure file     | :octicons-check-circle-fill-16:{ .req_optrec .scale_icon_medium } |           `pdb`         | Complex reference structure file (without hydrogens) with the desired assignment of chain ID and residue numbers |
+| Input File required            |                             Required                              |       Type        | Description                                                                                                      |
+|:-------------------------------|:-----------------------------------------------------------------:|:-----------------:|:-----------------------------------------------------------------------------------------------------------------|
+| Input parameters file          |    :octicons-check-circle-fill-16:{ .req .scale_icon_medium }     |       `in`        | Input file containing all the specifications regarding the type of calculation that is going to be performed     |
+| The MD Structure+mass(db) file |    :octicons-check-circle-fill-16:{ .req .scale_icon_medium }     |    `tpr` `pdb`    | Structure file containing the system coordinates                                                                 |
+| An index file                  |    :octicons-check-circle-fill-16:{ .req .scale_icon_medium }     |       `ndx`       | File containing the receptor and ligand in separated groups                                                      |
+| Receptor and ligand group      |    :octicons-check-circle-fill-16:{ .req .scale_icon_medium }     |    `integers`     | Group numbers in the index files                                                                                 |
+| A trajectory file              |    :octicons-check-circle-fill-16:{ .req .scale_icon_medium }     | `xtc` `pdb` `trr` | Final GROMACS MD trajectory, fitted and with no pbc.                                                             |
+| Ligand parameters file         |    :octicons-check-circle-fill-16:{ .req .scale_icon_medium }     |      `mol2`       | The Antechamber output  `mol2` file of ligand parametrization                                                    |
+| A topology file (not included) |  :octicons-check-circle-fill-16:{ .req_opt .scale_icon_medium }   |       `top`       | GROMACS topology file (The `* .itp` files defined in the topology must be in the same folder                     |
+| A Reference Structure file     | :octicons-check-circle-fill-16:{ .req_optrec .scale_icon_medium } |       `pdb`       | Complex reference structure file (without hydrogens) with the desired assignment of chain ID and residue numbers |
               
 :octicons-check-circle-fill-16:{ .req } -> Must be defined -- :octicons-check-circle-fill-16:{ .req_optrec } -> 
 Optional, but recommended -- :octicons-check-circle-fill-16:{ .req_opt } -> Optional
@@ -67,9 +67,21 @@ forcefields="oldff/leaprc.ff99SB,leaprc.gaff"
 &gb
 igb=1, saltcon=0.150,
 ifqnt=1, qm_theory=PM3,
-qm_residues="A/40-41,44,47,78,81-82,85,88,115,118,122,215,218-220,232 B/241"
-# qm_residues selection with "within" keyword (new in v1.5.0)
-#qm_residues="within 5"
+
+# Residues to be treated with QM can be selected using different approaches. Please, make sure to include at least 
+# one residue from both the receptor and ligand in the qm_residues mask when using 'ifqnt'. This requirement is 
+# automatically fulfilled when using the within keyword https://groups.google.com/g/gmx_mmpbsa/c/GNb4q4YGCH8
+
+# Residue selection by distance (recommended)
+qm_residues="within 4"
+
+## Explicit residue selection
+#qm_residues="A/40-41,44,47,78,81-82,85,88,115,118,122,215,218-220,232 B/241"
+
+# Residue selection with amber masks
+#com_qmmask="(:44,47,85,88,218&!@N,H,CA,HA,C,O) | :241"
+#rec_qmmask="(:44,47,85,88,218&!@N,H,CA,HA,C,O)"
+#lig_qmmask=":1"
 /
 ```
 

diff --git a/examples/QM_MMGBSA/mmpbsa.in b/examples/QM_MMGBSA/mmpbsa.in
@@ -1,7 +1,9 @@
 Sample input file for QM/MMGBSA calculation
-#This input file is meant to show only that gmx_MMPBSA works. Although, we tried to use the input files as recommended in the
-#Amber manual, some parameters have been changed to perform more expensive calculations in a reasonable amount of time. Feel free to change the parameters
-#according to what is better for your system.
+This input file is meant to show only that gmx_MMPBSA works.
+Although, we tried to use the input files as recommended in the
+Amber manual, some parameters have been changed to perform more
+expensive calculations in a reasonable amount of time. Feel free
+to change the parameters according to what is better for your system.
 
 &general
 sys_name="QM/MMGBSA",
@@ -10,14 +12,22 @@ endframe=14,
 PBRadii=2,
 forcefields="oldff/leaprc.ff99SB,leaprc.gaff"
 /
-#make sure to include at least one residue from both the receptor
-#and ligand in the qm_residues mask when using 'ifqnt'.
-#this requirement is automatically fulfilled when using the within keyword
-#https://groups.google.com/g/gmx_mmpbsa/c/GNb4q4YGCH8
 &gb
 igb=1, saltcon=0.150,
 ifqnt=1, qm_theory=PM3,
-qm_residues="A/40-41,44,47,78,81-82,85,88,115,118,122,215,218-220,232 B/241"
-# qm_residues selection with "within" keyword (new in v1.5.0)
-#qm_residues="within 5"
-/
+
+# Residues to be treated with QM can be selected using different approaches. Please, make sure to include at least
+# one residue from both the receptor and ligand in the qm_residues mask when using 'ifqnt'. This requirement is
+# automatically fulfilled when using the within keyword https://groups.google.com/g/gmx_mmpbsa/c/GNb4q4YGCH8
+
+# Residue selection by distance (recommended)
+qm_residues="within 4"
+
+## Explicit residue selection
+#qm_residues="A/40-41,44,47,78,81-82,85,88,115,118,122,215,218-220,232 B/241"
+
+# Residue selection with amber masks
+#com_qmmask="(:44,47,85,88,218&!@N,H,CA,HA,C,O) | :241"
+#rec_qmmask="(:44,47,85,88,218&!@N,H,CA,HA,C,O)"
+#lig_qmmask=":1"
+/