Recent changes to QuickStartGuide-AMBER

QuickStartGuide-AMBER modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 09 Dec 2024 02:23:24 -0000

--- v46
+++ v47
@@ -35,7 +35,7 @@
 ----

 This quick-start guide aims to calculate the solvation free energy of ethanol.
-Unpack the ermod data archive (https://sourceforge.net/projects/ermod/files/data_example/).
+Unpack the ERmod data archive (https://sourceforge.net/projects/ermod/files/data_example/).
 In the directory, there are several input files used in this guide.

 This guide uses the topology of ethanol existing in the archive, and does not show how to generate a new one.
@@ -122,7 +122,7 @@

 In the input file, *"`ioutfm = 1`" is specified*.
 This forces AMBER to write the "NetCDF" version of output trajectory.
-The file extension of the trajectory needs to be specified as ".nc", which is necessary to tell `ermod` that the file is in the NetCDF binary format.
+The file extension of the trajectory needs to be specified as ".nc", which is necessary to tell `erdst` that the file is in the NetCDF binary format.

 Example configuration files are available on https://sourceforge.net/projects/ermod/files/data_example/.
 MD production runs are performed in NPT condition, over 100 ps for the solution system to take 10,000 snapshots with 10 fs interval, and over 50 ps for the pure solvent to take 500 snapshots with 100 fs interval. An MD of isolated solute is done over 50 ns in addition, to take 500,000 snapshots with 100 fs interval. 
@@ -132,7 +132,7 @@
 Generate input configuration for solvation free energy calculation
 ----

-Input configuration file for ermod and slvfe will be generated via various helper scripts. First, execute the following command to generate system information:
+Input configuration file for erdst and slvfe will be generated via various helper scripts. First, execute the following command to generate system information:

 ~~~~
 (ERmod directory)/share/ermod/tools/AMBER/gen_structure --top etohsol.top

QuickStartGuide-AMBER modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 09 Dec 2024 02:21:18 -0000

--- v45
+++ v46
@@ -1,18 +1,18 @@
 Quick Start Guide for AMBER
 ====

-AMBER format is supported from ERmod 0.3.0.
-
-Building ERMOD plugin 
-----
-
-Since not all computer systems have the [NetCDF](http://www.unidata.ucar.edu/software/netcdf/), ERMOD does not contain a plugin file for the NetCDF file format, which is used in AMBER.
+AMBER format is supported as of ERmod 0.3.0.
+
+Building ERmod plugin 
+----
+
+Since not all computer systems have the [NetCDF](http://www.unidata.ucar.edu/software/netcdf/), ERmod does not contain a plugin file for the NetCDF file format, which is used in AMBER.
 Consult [VMD plugin build](build-VMDPlugin) to see how to compile the netcdf plugin.

 MD Preparation
 ----

-To use AMBER for ermod, user must compile AMBER with NetCDF support. *NetCDF support may not be enabled depending on user's environment!* If user does not understand what NetCDF is, stand back and read the AMBER manual.
+To use AMBER for ERmod, user must compile AMBER with NetCDF support. *NetCDF support may not be enabled depending on user's environment!* If user does not understand what NetCDF is, stand back and read the AMBER manual.

 Set environment to let AMBER know where AMBER is. If user's shell is `bash` or `zsh`,

QuickStartGuide-AMBER modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 07:51:10 -0000

--- v44
+++ v45
@@ -1,4 +1,4 @@
-Quick Start Guide for AMBER (ver. 0.3.x)
+Quick Start Guide for AMBER
 ====

 AMBER format is supported from ERmod 0.3.0.
@@ -52,34 +52,38 @@
 The contents of `etohsol.leap` read as:

 ~~~~
-     1 source leaprc.protein.ff19SB
-     2 loadAmberPrep etoh.prep
-     3 mol = loadPDB etoh.pdb
-     4 check mol
-     5 saveAmberParm mol etohiso.top etohiso.crd
-     6 
-     7 solvateBox mol TIP3PBOX 13.41
-     8 remove mol mol.1002
-     9 saveAmberParm mol etohsol.top etohsol.crd
-    10
-    12 remove mol mol.1
-    13 saveAmberParm mol water.top water.crd
-    14 quit
-~~~~
-
-Line 1 corresponds to the force field to be used; it is AMBER ff19SB in the above case.
-Line 2 corresponds to loading the AMBER parameter file for ethanol. File `etoh.prep` is included in the data archive downloaded.
-Line 5 prepares the input files for the MD of isolated ethanol.
-Line 7 creates a system of solvated ethanol. This example uses solvateBox command to create a cubic box of about 13.4 angstrom in size. The number of water molecules recommended to be added is about 1000, if the solute is small and its charge is absent or equal to 1 or -1.
-In the following line, a water molecule is removed just to set the number of solvent water molecules exactly to 1000.
-Line 9 prepares the input files for the MD of ethanol-water solution system.
-In Lines 12 and 13, the solute molecule (ethanol) is removed, and pure water box is prepared.
-
-When CMAP is used , gen_structure in the following part  will halt with an error message of
-~~~~
-    Error: failed to parse topology file. Is topology file correctly written?
-~~~~
-In such cases, user opens the topology file generated with tleap and deletes the lines of "%COMMENT ... CMAP" after "%FLAG CMAP_PARAMETER ..."
+1   # For Ambertools <= 15
+2   #source leaprc.ff99SB
+3   # For Ambertools >= 16
+4   source leaprc.protein.ff19SB
+5   # For Ambertools <= 19 next line may not be necessary
+6   source leaprc.water.tip3p
+7   loadAmberPrep etoh.prep
+8   mol = loadPDB etoh.pdb
+9   check mol
+10  saveAmberParm mol etohiso.top etohiso.crd
+11  
+12  # To get exactly 1000 molecules we can adjust the length and remove some unnecessary molecules
+13  # (Actually you do not have to do this, we just want to show how...)
+14  solvateBox mol TIP3PBOX 13.41
+15  remove mol mol.1002
+16  saveAmberParm mol etohsol.top etohsol.crd
+17  
+18  # We must have EXACTLY the same number of solvent molecules for both solution system and reference (pure solvent) system.
+19  # Thus we remove the solute to ensure they have the same number of solvents
+20  remove mol mol.1
+21  saveAmberParm mol water.top water.crd
+22  quit
+~~~~
+
+Line 4 corresponds to the force field to be used; it is AMBER ff19SB in the above case.
+Line 7 corresponds to loading the AMBER parameter file for ethanol. File `etoh.prep` is included in the data archive downloaded.
+Line 10 prepares the input files for the MD of isolated ethanol.
+Line 14 creates a system of solvated ethanol. This example uses solvateBox command to create a cubic box of about 13.4 angstrom in size. The number of water molecules recommended to be added is about 1000, if the solute is small and its charge is absent or equal to 1 or -1.
+In the following line, a water molecule is removed just to set the number of solvent water molecules exactly to 1000 (this is not necessary but just for demonstration purpose who want to reproduce)
+Line 16 prepares the input files for the MD of ethanol-water solution system.
+In Lines 20 and 21, the solute molecule (ethanol) is removed, and pure water box is prepared.
+

 Equilibration and production run
 ----
@@ -140,7 +144,7 @@
 In the example case, the ethanol molecule is the solute; type type "1" or “ETO” (do not include quotation marks) to proceed.
 After the execution, two directories are created, namely soln and refs.
 Inside these directories, `soln/MDinfo`, `soln/MolPrm1`, `soln/SltInfo`, `refs/MDinfo`, `refs/MolPrm1`, and `refs/SltInfo` files are generated.
-See [Parameter files for ermod](parameters-ermod03) for detailed description of SltInfo, MolPrm1, and so on.
+See [Parameter files for erdst](parameters-erdst) for detailed description of SltInfo, MolPrm1, and so on.

 soln/MDinfo should read as

@@ -158,7 +162,7 @@
 But the number of molecular species in refs/MDinfo is 1, since MDinfo in this case carries the information of the pure solvent system.

 Both in soln and refs directories, MolPrm1 and SltInfo should be found.
-MolPrm1 is the parameter file for solvent molecule, and SltInfo is the parameter file for solute. Both files contain the Lennard-Jones parameters and charge information, which are necessary in the calculation. See [Parameter files for ermod](parameters-ermod03) for detailed description of MDInfo, SltInfo, MolPrm1, and so on.
+MolPrm1 is the parameter file for solvent molecule, and SltInfo is the parameter file for solute. Both files contain the Lennard-Jones parameters and charge information, which are necessary in the calculation. See [Parameter files for erdst](parameters-erdst) for detailed description of MDInfo, SltInfo, MolPrm1, and so on.
 Finally, there is an LJTable file in each directory, which specifies the interaction energy table in AMBER.

 Now the parameters for the solution system are prepared.
@@ -172,13 +176,13 @@
 The trajectory (.nc == netcdf file) and log files are fed to the script.
 The options --traj and --log can be simplified to -x and -l, respectively. 
 After running the script, a symbolic link file, namely HISTORY, is to be created.
-A file named parameters_er is also to be created; this file controls how the ermod program runs.
+A file named parameters_er is also to be created; this file controls how the erdst program runs.
 MDinfo is further to be updated; “FRAME” on the first line is replaced by the number of snapshots in trajectory.

 Start the solute-solvent interaction calculation in the solution system with:

 ~~~~
-(ERmod directory)/bin/ermod
+(ERmod directory)/bin/erdst
 ~~~~

 If the program runs successfully, there should be files named engsln.xx and aveuv.tt, where xx is a two-digit integer, besides several other outputs.
@@ -194,7 +198,7 @@
 ~~~~
 cd ../refs
 (ERmod directory)/share/ermod/tools/AMBER/gen_input --traj ../solvent_run.nc --log ../solvent_run.mdout --flexible ../solute_run.nc
-(ERmod directory)/bin/ermod
+(ERmod directory)/bin/erdst
 ~~~~

 The first two arguments are to be taken similarly to the case of the solution (of course, the nc and log files are changed to those of pure solvent).
@@ -202,19 +206,19 @@
 The option --flexible can be simplified to -s.
 In addition to a symbolic link named HISTORY, a symbolic link file named SltConf is generated; HISTORY refers to the trajectory of the solvent, solvent_run.nc, and SltConf is linked to the trajectory file of the isolated solute, solute_run.nc.

-After running ermod, user obtains the energy distributions for the insertion operation.
+After running erdst, user obtains the energy distributions for the insertion operation.
 engref.xx is the histogram of the solute-solvent pair interaction energy at insertions in reference system, and corref.xx is the correlation matrix.
 User may notice that there are 5 outputs of energy distribution functions.
 This is because the reference trajectory is divided into 5 sections,
 and the output distribution functions are obtained from each of the 5 blocks.

-When two ermod runs are finished in the soln and refs directories, the solvation free energy can be calculated from the distribution functions obtained.
+When two erdst runs are finished in the soln and refs directories, the solvation free energy can be calculated from the distribution functions obtained.
 Go to [Quick Start Guide](QuickStartGuide) ---- Running slvfe: Getting Final Output.

 The trajectory is divided into a set of blocks both for soln and refs.
 The default value of the number of divisions is 10 for the solution system and is 5 for the reference.
-The number of divisions can be modified with the numdiv parameter in the parameters_er file when the ermod program is run.
-See [Parameter files for ermod](parameters-ermod03) for the description of the parameters which can be specified in parameters_er.
+The number of divisions can be modified with the numdiv parameter in the parameters_er file when the erdst program is run.
+See [Parameter files for erdst](parameters-erdst) for the description of the parameters which can be specified in parameters_er.

 If the solute is rigid (its intramolecular structure is fixed), the procedure is simplified.
 The scheme for the solution part is the same as above.
@@ -226,12 +230,12 @@
 ~~~~
 cd ../refs
 (ERmod directory)/share/ermod/tools/AMBER/gen_input --traj ../solvent_run.nc --log ../solvent_run.mdout --rigid ../etoh.pdb
-(ERmod directory)/bin/ermod
+(ERmod directory)/bin/erdst
 ~~~~

 The difference from the flexible solute case is the third argument.
 The third argument, --rigid, specifies that the test-particle insertion calculation is performed with fixed structure of the solute.
 The option --rigid can be simplified to -r.
 The structure of the solute is taken from the SltInfo file when the solute is rigid.
-See [Parameter files for ermod](parameters-ermod03) for the format of the SltInfo file in the case of rigid solute.
+See [Parameter files for erdst](parameters-erdst) for the format of the SltInfo file in the case of rigid solute.
 When the refs calculation is done, the calculation of solvation free energy of rigid solute can be done with the same procedure as that in the flexible case.

QuickStartGuide-AMBER modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 09 Jun 2023 08:43:29 -0000

--- v43
+++ v44
@@ -75,7 +75,7 @@
 Line 9 prepares the input files for the MD of ethanol-water solution system.
 In Lines 12 and 13, the solute molecule (ethanol) is removed, and pure water box is prepared.

-When CMAP is used, , gen_structure in the following part  will halt with an error message of
+When CMAP is used , gen_structure in the following part  will halt with an error message of
 ~~~~
     Error: failed to parse topology file. Is topology file correctly written?
 ~~~~

QuickStartGuide-AMBER modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 09 Jun 2023 08:38:38 -0000

--- v42
+++ v43
@@ -67,7 +67,7 @@
     14 quit
 ~~~~

-Line 1 corresponds to the force field to be used: in this case AMBER ff99 with correction to main-chain dihedral angles.
+Line 1 corresponds to the force field to be used; it is AMBER ff19SB in the above case.
 Line 2 corresponds to loading the AMBER parameter file for ethanol. File `etoh.prep` is included in the data archive downloaded.
 Line 5 prepares the input files for the MD of isolated ethanol.
 Line 7 creates a system of solvated ethanol. This example uses solvateBox command to create a cubic box of about 13.4 angstrom in size. The number of water molecules recommended to be added is about 1000, if the solute is small and its charge is absent or equal to 1 or -1.

QuickStartGuide-AMBER modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 09 Jun 2023 08:36:41 -0000

--- v41
+++ v42
@@ -103,7 +103,6 @@

 ######solvent system######
 ~~~~
-::::sh
 sander -i min.mdin -o solvent_min.mdout -p water.top -c water.crd -r solvent_min.crd -x solvent_min.nc -inf solvent_min.mdinfo -O 
 pmemd -i nvt.mdin -o solvent_nvt.mdout -p water.top -c solvent_min.crd -r solvent_nvt.crd -x solvent_nvt.nc -inf solvent_nvt.mdinfo -O
 pmemd -i npt.mdin -o solvent_npt.mdout -p water.top -c solvent_nvt.crd -r solvent_npt.crd -x solvent_npt.nc -inf solvent_npt.mdinfo -O
@@ -112,7 +111,6 @@

 ######isolated solute system######
 ~~~~
-::::sh
 sander -i solute_min.mdin -o solute_min.mdout -p etohiso.top -c etohiso.crd -r solute_min.crd -x solute_min.nc -inf solute_min.mdinfo -O 
 sander -i solute_eq.mdin -o solute_eq.mdout -p etohiso.top -c solute_min.crd -r solute_eq.crd -x solute_eq.nc -inf solute_eq.mdinfo -O
 sander -i solute_run.mdin -o solute_run.mdout -p etohiso.top -c solute_eq.crd -r solute_run.crd -x solute_run.nc -inf solute_run.mdinfo -O
@@ -133,7 +131,6 @@
 Input configuration file for ermod and slvfe will be generated via various helper scripts. First, execute the following command to generate system information:

 ~~~~
-::::sh
 (ERmod directory)/share/ermod/tools/AMBER/gen_structure --top etohsol.top
 ~~~~

@@ -148,7 +145,6 @@
 soln/MDinfo should read as

 ~~~~
-::::text
 FRAME 2
 1 1000
 9 3
@@ -169,7 +165,6 @@
 Move to soln directory and run the helper script:

 ~~~~
-::::sh
 cd soln
 (ERmod directory)/share/ermod/tools/AMBER/gen_input --traj ../solution_run.nc --log ../solution_run.mdout
 ~~~~
@@ -183,7 +178,6 @@
 Start the solute-solvent interaction calculation in the solution system with:

 ~~~~
-::::sh
 (ERmod directory)/bin/ermod
 ~~~~

@@ -198,7 +192,6 @@
 Then move on to refs directory to start calculating the reference part.

 ~~~~
-::::sh
 cd ../refs
 (ERmod directory)/share/ermod/tools/AMBER/gen_input --traj ../solvent_run.nc --log ../solvent_run.mdout --flexible ../solute_run.nc
 (ERmod directory)/bin/ermod
@@ -231,7 +224,6 @@
 In the refs directory, run the helper script:

 ~~~~
-::::sh
 cd ../refs
 (ERmod directory)/share/ermod/tools/AMBER/gen_input --traj ../solvent_run.nc --log ../solvent_run.mdout --rigid ../etoh.pdb
 (ERmod directory)/bin/ermod

QuickStartGuide-AMBER modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 09 Jun 2023 08:35:45 -0000

--- v40
+++ v41
@@ -45,7 +45,6 @@
 Feed it into `tleap` to generate the input topology:

 ~~~~
-::::sh
 tleap -f etohsol.leap
 ~~~~

@@ -53,7 +52,6 @@
 The contents of `etohsol.leap` read as:

 ~~~~
-::::text
      1 source leaprc.protein.ff19SB
      2 loadAmberPrep etoh.prep
      3 mol = loadPDB etoh.pdb
@@ -97,7 +95,6 @@

 ######solution system######
 ~~~~
-::::sh
 sander -i min.mdin -o solution_min.mdout -p etohsol.top -c etohsol.crd -r solution_min.crd -x solution_min.nc -inf solution_min.mdinfo -O 
 pmemd -i nvt.mdin -o solution_nvt.mdout -p etohsol.top -c solution_min.crd -r solution_nvt.crd -x solution_nvt.nc -inf solution_nvt.mdinfo -O
 pmemd -i npt.mdin -o solution_npt.mdout -p etohsol.top -c solution_nvt.crd -r solution_npt.crd -x solution_npt.nc -inf solution_npt.mdinfo -O

QuickStartGuide-AMBER modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 09 Jun 2023 08:35:15 -0000

--- v39
+++ v40
@@ -17,7 +17,6 @@
 Set environment to let AMBER know where AMBER is. If user's shell is `bash` or `zsh`,

 ~~~~
-::::sh
 export AMBERHOME=(path to AMBER)
 export PATH=$AMBERHOME/exe:$PATH
 ~~~~ 
@@ -25,7 +24,6 @@
 or if the shell is `csh` or `tcsh`,

 ~~~~
-::::csh
 setenv AMBERHOME (path to AMBER)
 setenv PATH $AMBERHOME/exe:$PATH
 ~~~~

QuickStartGuide-AMBER modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 09 Jun 2023 08:28:23 -0000

--- v38
+++ v39
@@ -81,7 +81,6 @@

 When CMAP is used, , gen_structure in the following part  will halt with an error message of
 ~~~~
-::::text
     Error: failed to parse topology file. Is topology file correctly written?
 ~~~~
 In such cases, user opens the topology file generated with tleap and deletes the lines of "%COMMENT ... CMAP" after "%FLAG CMAP_PARAMETER ..."

QuickStartGuide-AMBER modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 09 Jun 2023 08:27:56 -0000

--- v37
+++ v38
@@ -80,8 +80,11 @@
 In Lines 12 and 13, the solute molecule (ethanol) is removed, and pure water box is prepared.

 When CMAP is used, , gen_structure in the following part  will halt with an error message of
-     Error: failed to parse topology file. Is topology file correctly written
-In such cases, user opens the topology file generated with tleap and deletes the lines of "%COMMENT ... CMAP" after "%FLAG CMAP_PARAMETER_0X"
+~~~~
+::::text
+    Error: failed to parse topology file. Is topology file correctly written?
+~~~~
+In such cases, user opens the topology file generated with tleap and deletes the lines of "%COMMENT ... CMAP" after "%FLAG CMAP_PARAMETER ..."

 Equilibration and production run
 ----