Common applications of the MMTSB toolset - Revision history

Edit: /* Patching residues: */

2009-10-02T17:29:28Z

Patching residues:

Edit: /* Patching residues: */

2009-07-22T17:07:36Z

Patching residues:

Edit: /* Patching residues: */

2009-07-22T15:59:47Z

Patching residues:

Edit: /* For more examples: */

2009-07-22T15:50:19Z

For more examples:

Edit: /* Running and analyzing protein simulations with replica-exchange: */

2009-07-20T16:00:01Z

Running and analyzing protein simulations with replica-exchange:

Edit: /* Running and analyzing protein simulations with replica-exchange: */

2009-07-20T15:57:44Z

Running and analyzing protein simulations with replica-exchange:

Edit: /* Running and analyzing protein simulations with replica-exchange: */

2009-07-20T15:54:07Z

Running and analyzing protein simulations with replica-exchange:

Edit: /* Running and analyzing protein simulations with replica-exchange: */

2009-07-20T15:52:50Z

Running and analyzing protein simulations with replica-exchange:

Edit: /* Running and analyzing protein simulations with replica-exchange: */

2009-07-20T15:50:49Z

Running and analyzing protein simulations with replica-exchange:

Edit: /* Running and analyzing protein simulations with replica-exchange: */

2009-07-20T15:49:46Z

Running and analyzing protein simulations with replica-exchange:

@@ Line 328: / Line 328: @@
 Situations may arise where standard residues need to be modified in a simulation. Standard patches are provided in the CHARMM files for creating disulfide bonds (DISU), protonating an aspartate residue (ASPP) or deprotonating a or blocking chain termini residues.
 These residues can be patched automatically in any of the MMTSB tools that take [-par [http://feig.bch.msu.edu/mmtsb/CHARMM_Parameters CHARMMparams]] or [-mdpar [http://feig.bch.msu.edu/mmtsb/CHARMM_Parameters CHARMMparams]] options. The general format for a single patch is:
-   -par <patchname>:<segid>.<resid>
+   -par PATCH=<patchname>:<segid>.<resid>
 The general format for a disulfide bond is:
-   -par DISU:<segid1>.<resid1>:<segid2>.<resid2>
+   -par PATCH=DISU:<segid1>.<resid1>:<segid2>.<resid2>
 Multiple patches must be separated by "_", for example:
-   -par <patchname1>:<segid1>.<resid1>_<patchname2>:<segid2>.<resid2>_<patchname3>:<segid3>.<resid3>
+   -par PATCH=<patchname1>:<segid1>.<resid1>_<patchname2>:<segid2>.<resid2>_<patchname3>:<segid3>.<resid3>
 Here's an example of how residue patching might be used in a project. Starting from a PDB file [http://www.pdb.org/pdb/explore/explore.do?structureId=1BG8 1BG8], we convert it into CHARMM27 format, complete with added hydrogen atoms and blocked termini:

@@ Line 334: / Line 334: @@
    -par <patchname1>:<segid1>.<resid1>_<patchname2>:<segid2>.<resid2>_<patchname3>:<segid3>.<resid3>
-Starting from a PDB file [http://www.pdb.org/pdb/explore/explore.do?structureId=1BG8 1BG8], we convert it into CHARMM27 format, complete with added hydrogen atoms and blocked termini:
+Here's an example of how residue patching might be used in a project. Starting from a PDB file [http://www.pdb.org/pdb/explore/explore.do?structureId=1BG8 1BG8], we convert it into CHARMM27 format, complete with added hydrogen atoms and blocked termini:
    convpdb.pl -chain A -segnames 1BG8.pdb > 1BG8_a.pdb
    convpdb.pl -chain B 1BG8.pdb > 1BG8_b.pdb

@@ Line 327: / Line 327: @@
 ==Patching residues:==
 Situations may arise where standard residues need to be modified in a simulation. Standard patches are provided in the CHARMM files for creating disulfide bonds (DISU), protonating an aspartate residue (ASPP) or deprotonating a or blocking chain termini residues.
-These residues can be patched automatically in any of the MMTSB tools that take [-par [[CHARMM_Parameters]]] or [-mdpar [[CHARMM_Parameters]]] options. The general format for a single patch is:
+These residues can be patched automatically in any of the MMTSB tools that take [-par [http://feig.bch.msu.edu/mmtsb/CHARMM_Parameters CHARMMparams]] or [-mdpar [http://feig.bch.msu.edu/mmtsb/CHARMM_Parameters CHARMMparams]] options. The general format for a single patch is:
    -par <patchname>:<segid>.<resid>
 The general format for a disulfide bond is:
@@ Line 353: / Line 353: @@
 BG8_dimer_min.pdb > 1BG8_dimer_md.pdb
 These same -par patch options can be used in energy calculations with [[enerCHARMM.pl]], for running Constant-pH simulations with replica-exchange simulations via [[aarex.pl]], etc.<br>
-Note: for MMTSB commands which use -mdpar options (like [[aarex.pl]]) instead of -par options, the syntax is identical.
+Note: for MMTSB commands which use -mdpar options (like [[aarex.pl]]) instead of -par options, the syntax of the patch option is identical.
 <br><br>
 The patches that are currently available (top_all27_prot_na.rtf) are:

@@ Line 324: / Line 324: @@
 For a more thorough description, see the [http://www.mmtsb.org/workshops/mmtsb-ctbp_2006/Tutorials/MMTSB_PBCalculations/MMTSBPBCalculations.html MMTSB Tool Set - Continuum electrostatics calculations tutorial].
 <br><br><br>
 ==For more examples:==
 Download and follow  [http://www.mmtsb.org/workshops/mmtsb-ctbp_2006/Tutorials/WorkshopTutorials_2006.html tutorials]  that were prepared for past MMTSB workshops.

@@ Line 295: / Line 295: @@
   rexinfo.pl -byclient aa1 -dir gbrex
-The command to examine how the temperature varies for a given replica
+"Client" means replica here, and for all-atom replica exchange simulations, the replicas are named aa1 through aaN.
- rexinfo.pl -byclient aa1
+Another way to query the replica exchange output is to look at which clients are at the lowest temperature at each cycle
-"Client" means replica here, and for all-atom replica exchange simulations, the replicas are named aa1 through aaN.
+ rexinfo.pl -bytemp 300
 If the archive parameter was specified during the replica exchange run, all of the conformations are stored in a single file (prod.coor.archive). They can be accessed with readArchive.pl. An example of how to use this tool is given in the following:

@@ Line 293: / Line 293: @@
 The command to look at the energy and temperature profiles of each replica
-  rexinfo -byclient aa1 -dir gbrex
+  rexinfo.pl -byclient aa1 -dir gbrex
 The command to examine how the temperature varies for a given replica

@@ Line 271: / Line 271: @@
 The script to prepare the extended structure of the protein is called [[protein.inp]]
-Run the following command to obtain the protein configurations (pept.pdb and helix.pdb) to be used is replica exchange simulations
+Run the following command to obtain the protein configurations (pept.pdb and helix.pdb) to be used in replica exchange simulations
   $CHARMMEXEC < protein.inp > protein.out

←Older revision		Revision as of 15:50, 20 July 2009
Line 310:		Line 310:

	For a more thorough description, see the [http://www.mmtsb.org/workshops/mmtsb-ctbp_2006/Tutorials/REX_GBMembFold_Tutorial/REX_Analysis.html MMTSB Tool Set - Analysis of replica exchange simulations].		For a more thorough description, see the [http://www.mmtsb.org/workshops/mmtsb-ctbp_2006/Tutorials/REX_GBMembFold_Tutorial/REX_Analysis.html MMTSB Tool Set - Analysis of replica exchange simulations].
		+	<br><br>

	==Generating and visualizing the electrostatic surface potential of a macromolecule:==		==Generating and visualizing the electrostatic surface potential of a macromolecule:==

@@ Line 265: / Line 265: @@
 ==Running and analyzing protein simulations with replica-exchange:==
-First we prepare a protein of 16 residues as an extended using Charmm commands. We will then use this protein as the input pdb for the replica exchange simulations in GBSW implicit solvent model. The replica exchange simulation example runs the protein at 4 different temperatures simultaneously using 4 different processors.
+First we prepare a protein of 16 residues as an extended structure using Charmm. We will then use this protein as the input pdb file for replica exchange simulations in GBSW implicit solvent model. The replica exchange simulation performs molecular dynamics at 4 different temperatures simultaneously using 4 different processors.
 '''1) Running Replica Exchange simulations'''
@@ Line 275: / Line 275: @@
   $CHARMMEXEC < protein.inp > protein.out
-Next we use the following aarex.pl from MMTSB toolset to run the replica exchange simulations at 4 different temperature windows using the GBSW implicit solvent model.
+Next we use the following perl script from MMTSB toolset to run the replica exchange simulations at 4 different temperature windows using the GBSW implicit solvent model.
 Note : The last line of the command shows that 4 replica will be run at different temperatures between 300 and 400 K.
@@ Line 285: / Line 285: @@
           -temp 4:300:400 pept.pdb
-Note that the machine in which you are running should have 4 processors or you could run the simulation in a cluster by requesting 4 processors.
+Note that the machine in which you are running should have atleast 4 processors or you could run the simulation in a cluster by requesting 4 processors.
 '''2) Analysis of Replica exchange results'''
@@ Line 295: / Line 295: @@
   rexinfo -byclient aa1 -dir gbrex
-The command to examine how the temperature varies for a given replica with:
+The command to examine how the temperature varies for a given replica:
   rexinfo.pl -byclient aa1