import>Jmc49 at 11:25, 29 June 2011

2011-06-29T11:25:49Z

← Older revision		Revision as of 11:25, 29 June 2011
Line 227:		Line 227:
	This PDB file can then be used to generate a '''perm.allow''' file:		This PDB file can then be used to generate a '''perm.allow''' file:
	<pre>		<pre>
	~/svn/SCRIPTS/make_perm.allow/perm-pdb.py alaphe_min1_amber_ter.pdb		~/svn/SCRIPTS/make_perm.allow/perm-pdb.py alaphe_min1_amber_ter.pdb AMBER
	</pre>		</pre>

			Note the new (as of commit number 22238, 10th June 2011) requirement for specification of whether we are using amber or charmm, as the numbering/residue labelling differs.

	You should now have a perm.allow file :)		You should now have a perm.allow file :)

import>Ss2029: /* Symmetrising the AMBER topology file */

2011-04-26T12:23:52Z

Symmetrising the AMBER topology file

← Older revision		Revision as of 12:23, 26 April 2011
Line 203:		Line 203:
	</pre>		</pre>

	The format used here is that each residue has 4 spaces in the file. To specify termini, you need to change the N-terminal ALA to '''NALA''' and the C-terminal PHE to 'CPHE', maintaining this format. ~~Her~~ is what it should look like:		The format used here is that each residue has 4 spaces in the file. To specify termini, you need to change the N-terminal ALA to '''NALA''' and the C-terminal PHE to 'CPHE', maintaining this format. Here is what it should look like:
	<pre>		<pre>
	%FLAG RESIDUE_LABEL		%FLAG RESIDUE_LABEL

import>Ss2029: /* Using PDBs from other sources */

2011-04-26T12:10:35Z

Using PDBs from other sources

← Older revision		Revision as of 12:10, 26 April 2011
Line 175:		Line 175:

	<pre>		<pre>
	source leaprc.~~ff99~~		source leaprc.ff99SB
	set default PBradii mbondi2		set default PBradii mbondi2
	peptide = loadpdb alaphe_min1_amber.pdb		peptide = loadpdb alaphe_min1_amber.pdb

import>Jmc49: New page: Before we can do anything, we need to set up our system. == Creating AMBER input files == === Using LEaP (from scratch) === If you're going to use GMIN to find conformations to conn...

2011-03-14T14:49:00Z

New page: Before we can do anything, we need to set up our system. == Creating AMBER input files == === Using LEaP (from scratch) === If you're going to use GMIN to find conformations to conn...

New page

Before we can do anything, we need to set up our system.

== Creating AMBER input files ==

=== Using LEaP (from scratch) ===

If you're going to use [[GMIN]] to find conformations to connect (for example with a small peptide) - and you don't care too much about the initial structure, you can generate it in LEaP. For the ALA-PHE peptide we're looking at here, the following LEaP input should do!

<pre>
source leaprc.ff99SB
set default PBradii mbondi2
peptide = sequence {NALA CPHE}
savepdb peptide alaphe.pdb
saveamberparm peptide coords.prmtop.old coords.inpcrd
quit
</pre>

This LEaP script does the following line by line:
* load the ff99SB forcefield parameters and atom types
* set the Poisson-Boltzmann radii for atom to the mbondi2 set (appropriate for use with igb=2 and igb=5 options in AMBER)
* create a '''peptide''' object with amino acid sequence ALA-PHE where ALA is at the N-terminus and PHE is at the C-terminus. The peptide is created linear with all bond lengths and angles set to their [[AMBER]] defaults.
* save a PDB file called '''alaphe.pdb''' of the '''peptide''' object so we can easily visualise the initial conformation
* save an AMBER topology file (coords.prmtop.old) and coordinate file (coords.inpcrd) for the '''peptide''' object

You can run this leap script as follows:
<pre>
tleap -f tleap.in
</pre>

=== Using PDBs from other sources ===

When you first get PDBs either from a database, or another source, they often will not be using the atom naming conventions AMBER will be expecting. As a result, you need to do some preparation either manually renaming atoms, or preferably - using '''protonate''', an [[AMBER]] program.

For this tutorial, we're going to be using a folded and unfolded structure for the dipeptide ALA-PHE. Here are the initial PDBs:

'''alaphe_min1.pdb'''
<pre>
REMARK NALA
ATOM 1 N ALA 1 4.690 2.524 1.502
ATOM 2 1H ALA 1 5.123 1.608 1.471
ATOM 3 2H ALA 1 4.064 2.608 2.285
ATOM 4 2H ALA 1 5.478 3.159 1.619
ATOM 5 CA ALA 1 4.023 2.813 0.213
ATOM 6 HA ALA 1 3.141 2.178 0.136
ATOM 7 CB ALA 1 3.567 4.278 0.132
ATOM 8 1HB ALA 1 4.417 4.951 0.261
ATOM 9 2HB ALA 1 3.103 4.465 -0.837
ATOM 10 3HB ALA 1 2.836 4.479 0.916
ATOM 11 C ALA 1 4.949 2.387 -0.927
ATOM 12 O ALA 1 4.840 1.244 -1.353
ATOM 13 N PHE 2 5.909 3.231 -1.323
ATOM 14 H PHE 2 5.754 4.207 -1.120
ATOM 15 CA PHE 2 7.293 2.871 -0.989
ATOM 16 HA PHE 2 7.512 1.851 -1.311
ATOM 17 CB PHE 2 8.262 3.844 -1.679
ATOM 18 2HB PHE 2 8.096 3.798 -2.756
ATOM 19 3HB PHE 2 8.038 4.862 -1.355
ATOM 20 CG PHE 2 9.726 3.561 -1.399
ATOM 21 CD1 PHE 2 10.475 2.762 -2.283
ATOM 22 HD1 PHE 2 10.004 2.342 -3.160
ATOM 23 CE1 PHE 2 11.834 2.503 -2.025
ATOM 24 HE1 PHE 2 12.406 1.886 -2.704
ATOM 25 CZ PHE 2 12.447 3.041 -0.879
ATOM 26 HZ PHE 2 13.489 2.838 -0.676
ATOM 27 CE2 PHE 2 11.700 3.835 0.009
ATOM 28 HE2 PHE 2 12.165 4.240 0.896
ATOM 29 CD2 PHE 2 10.342 4.094 -0.251
ATOM 30 HD2 PHE 2 9.763 4.693 0.439
ATOM 31 C PHE 2 7.386 2.911 0.540
ATOM 32 O PHE 2 6.994 3.978 1.066
ATOM 33 OXT PHE 2 7.287 1.835 1.161
TER
END
</pre>

'''alaphe_min2.pdb'''
<pre>
REMARK NALA
ATOM 1 N ALA 1 4.769 2.964 -0.028
ATOM 2 1H ALA 1 4.610 1.986 0.154
ATOM 3 2H ALA 1 3.983 3.392 -0.491
ATOM 4 2H ALA 1 4.904 3.417 0.875
ATOM 5 CA ALA 1 5.999 3.139 -0.824
ATOM 6 HA ALA 1 6.830 2.724 -0.257
ATOM 7 CB ALA 1 5.914 2.366 -2.148
ATOM 8 1HB ALA 1 5.813 1.299 -1.945
ATOM 9 2HB ALA 1 5.058 2.705 -2.732
ATOM 10 3HB ALA 1 6.824 2.528 -2.726
ATOM 11 C ALA 1 6.286 4.634 -1.024
ATOM 12 O ALA 1 5.759 5.213 -1.967
ATOM 13 N PHE 2 7.073 5.319 -0.182
ATOM 14 H PHE 2 7.180 6.295 -0.410
ATOM 15 CA PHE 2 7.613 4.889 1.130
ATOM 16 HA PHE 2 7.722 5.785 1.741
ATOM 17 CB PHE 2 9.033 4.298 0.978
ATOM 18 2HB PHE 2 9.713 5.116 0.738
ATOM 19 3HB PHE 2 9.348 3.908 1.948
ATOM 20 CG PHE 2 9.226 3.211 -0.070
ATOM 21 CD1 PHE 2 9.116 1.852 0.281
ATOM 22 HD1 PHE 2 8.888 1.580 1.304
ATOM 23 CE1 PHE 2 9.287 0.851 -0.692
ATOM 24 HE1 PHE 2 9.205 -0.191 -0.412
ATOM 25 CZ PHE 2 9.580 1.203 -2.021
ATOM 26 HZ PHE 2 9.725 0.433 -2.766
ATOM 27 CE2 PHE 2 9.702 2.559 -2.375
ATOM 28 HE2 PHE 2 9.937 2.831 -3.395
ATOM 29 CD2 PHE 2 9.527 3.559 -1.401
ATOM 30 HD2 PHE 2 9.629 4.600 -1.674
ATOM 31 C PHE 2 6.612 4.042 1.930
ATOM 32 O PHE 2 5.489 4.562 2.089
ATOM 33 OXT PHE 2 6.759 2.807 1.993
TER
END
</pre>

'''NOTE: from now on, I will only describe the preparation process for alaphe_min1.pdb - it is IDENTICAL for min2!

'''protonate''' (with the -k flag) reads through a PDB and replaces any hydrogen atoms it does not recognise with their AMBER equivalents. If you have AMBER installed, have set the $AMBERHOME variable and have included $AMBERHOME/exe in your $PATH - you should just be able to run it like this:

<pre>
protonate -k -i alaphe_min1.pdb -o alaphe_min1_amber.pdb
</pre>

If not, and you have access to clust, you can use my version:

<pre>
clust:~csw34/AMBER/amber9/exe/protonate
</pre>

Here is the output:

'''alaphe_min1_amber.pdb'''
<pre>
ATOM 1 N ALA 1 4.690 2.524 1.502
ATOM 2 H1 ALA 1 5.123 1.608 1.471
ATOM 3 H2 ALA 1 5.478 3.159 1.619
ATOM 4 H3 ALA 1 4.064 2.608 2.285
ATOM 5 CA ALA 1 4.023 2.813 0.213
ATOM 6 HA ALA 1 3.141 2.178 0.136
ATOM 7 CB ALA 1 3.567 4.278 0.132
ATOM 8 1HB ALA 1 2.836 4.479 0.916
ATOM 9 2HB ALA 1 4.417 4.951 0.261
ATOM 10 3HB ALA 1 3.103 4.465 -0.837
ATOM 11 C ALA 1 4.949 2.387 -0.927
ATOM 12 O ALA 1 4.840 1.244 -1.353
ATOM 13 N PHE 2 5.909 3.231 -1.323
ATOM 14 H PHE 2 5.754 4.207 -1.120
ATOM 15 CA PHE 2 7.293 2.871 -0.989
ATOM 16 HA PHE 2 7.512 1.851 -1.311
ATOM 17 CB PHE 2 8.262 3.844 -1.679
ATOM 18 3HB PHE 2 8.038 4.862 -1.355
ATOM 19 2HB PHE 2 8.096 3.798 -2.756
ATOM 20 CG PHE 2 9.726 3.561 -1.399
ATOM 21 CD1 PHE 2 10.475 2.762 -2.283
ATOM 22 HD1 PHE 2 10.004 2.342 -3.160
ATOM 23 CE1 PHE 2 11.834 2.503 -2.025
ATOM 24 HE1 PHE 2 12.406 1.886 -2.704
ATOM 25 CZ PHE 2 12.447 3.041 -0.879
ATOM 26 HZ PHE 2 13.489 2.838 -0.676
ATOM 27 CE2 PHE 2 11.700 3.835 0.009
ATOM 28 HE2 PHE 2 12.165 4.240 0.896
ATOM 29 CD2 PHE 2 10.342 4.094 -0.251
ATOM 30 HD2 PHE 2 9.763 4.693 0.439
ATOM 31 C PHE 2 7.386 2.911 0.540
ATOM 32 O PHE 2 6.994 3.978 1.066
ATOM 33 OXT PHE 2 7.287 1.835 1.161
END
</pre>

Now we're good to create some AMBER input using LEaP.

Now that we have a PDB using the [[AMBER]] naming conventions, we can load it into LEaP to create topology and coordinate files for the forcefield we're going to be using. For this tutorial, we'll use the '''ff99SB''' forcefield and we will be aiming to use the '''igb=2''' GB solvent model (see the AMBER9 manual!). It is important to know which solvent model we will be using in advance as it affects how we create our initial [[AMBER]] input.

Again, assuming you have [[AMBER]] installed - you can use '''tleap''' to generate the input you need. First, create a '''tleap.in''' file containing the following:

<pre>
source leaprc.ff99
set default PBradii mbondi2
peptide = loadpdb alaphe_min1_amber.pdb
saveamberparm peptide coords.prmtop.old coords.inpcrd
quit
</pre>

This LEaP script does the following line by line:
* load the ff99SB forcefield parameters and atom types
* set the Poisson-Boltzmann radii for atom to the mbondi2 set (appropriate for use with igb=2 and igb=5 options in AMBER)
* load the '''alaphe_min1_amber.pdb''' PDB into LEaP as object '''peptide'''
* save an AMBER topology file (coords.prmtop.old) and coordinate file (coords.inpcrd) for the '''peptide''' object

You can run this leap script as follows:
<pre>
tleap -f tleap.in
</pre>

== Symmetrising the AMBER topology file ==

To make sure that the improper dihedral angle energies are permutationally invariant, we need to run a script to symmetrise them. Firstly though, we need to modify the '''coords.prmtop.old''' file to make sure the script is able to identify termini correctly (the improper dihedrals for terminal residues are different!). In this case, it's quite easy as there are only two residues - both of which are terminal. Open up '''coords.prmtop.old''' in your favourite editor, and find the section that looks like this:
<pre>
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
ALA PHE
%FLAG RESIDUE_POINTER
</pre>

The format used here is that each residue has 4 spaces in the file. To specify termini, you need to change the N-terminal ALA to '''NALA''' and the C-terminal PHE to 'CPHE', maintaining this format. Her is what it should look like:
<pre>
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
NALACPHE
%FLAG RESIDUE_POINTER
</pre>

If you have the SVN repository checked-out in your home directory, you can run the symmetrisation script as follows:
<pre>
~/svn/SCRIPTS/AMBER/symmetrise_prmtop/perm-prmtop.ff03.py coords.prmtop.old coords.prmtop
</pre>

Assuming that worked without errors, you can then open up the new '''coords.prmtop''' file and change the residue labels back from NALA to '''ALA''' and CPHE to '''PHE'''. That's it, you have a topology file ready to go. Just one more thing before we start running things - we need to make a '''perm.allow''' file for later.

=== Making a perm.allow file for later ===

The perm.allow file specifies which groups can be permuted when aligning endpoints of paths. For example, it ensures that all three H atoms of CH3 are treated as being the same, so CH3 rotation does not affect alignment. To make a '''perm.allow''' file, we need a PDB that includes the termini being specified. This means we cannot use the original PDB. We could in this case just change ALA to '''NALA''' and PHE to '''CPHE''' in the PDB manually, but you can do it automatically using the '''coords.prmtop.old''' file we made earlier which still has the termini specified. We do this using the '''ambpdb''' program:
<pre>
ambpdb -p coords.prmtop.old < coords.inpcrd > alaphe_min1_amber_ter.pdb
</pre>

This PDB file can then be used to generate a '''perm.allow''' file:
<pre>
~/svn/SCRIPTS/make_perm.allow/perm-pdb.py alaphe_min1_amber_ter.pdb
</pre>

You should now have a perm.allow file :)

Setting up - Revision history

import>Jmc49 at 11:25, 29 June 2011

import>Ss2029: /* Symmetrising the AMBER topology file */

import>Ss2029: /* Using PDBs from other sources */

import>Jmc49: New page: Before we can do anything, we need to set up our system. == Creating AMBER input files == === Using LEaP (from scratch) === If you're going to use GMIN to find conformations to conn...