In earlier post we saw how we create pdb files for the structures we want to consider for multi component molecular dynamics analysis.
So now we have say PDB files for four structures - an aldehyde, nitrile, amine and a phenol molecule.
Now, In the first step we generate the prepin files for all these molecules by using:
$AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo prepi -c bcc -s 2
Here the molecules are neutral in nature. If you are working with ionic systems you need to add -nc flag in the end followed by charge of the moelcule.
So, if the moelcule has +1 charge, the command will be:
$AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo prepi -c bcc -s 2 -nc 1
If it is -1, command is:
$AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo prepi -c bcc -s 2 -nc -1
If you have followed earlier preocedure properly then your prepin file should be created in no time.
You can see some lines of a prepin file as an example created for the amine molecule :
----------------------------------
0 0 2
This is a remark line
molecule.res
MTL INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 C1 c3 M 3 2 1 1.540 111.208 180.000 0.14735
5 H12 h1 E 4 3 2 1.071 164.526 20.274 0.04281
6 H13 h1 E 4 3 2 1.069 63.986 -47.277 0.04290
7 H14 h1 E 4 3 2 1.070 62.998 84.283 -0.00841
8 N1 n3 M 4 3 2 1.009 85.966 -161.349 -0.91927
9 H11 hn E 8 4 3 1.011 109.459 -119.526 0.34729
10 H2 hn E 8 4 3 1.011 109.497 0.433 0.34733
-----------------------------
What is worth noting here is the word following line "molecule.res".
The three letters "MTL" defines the unit for the molecule. When you create the prepin file for a molecule in a set of molecules to be cosidered together in a calculation, it is always suggested to open the prepin file and check this unit name.
First of all, it is better if it is a 3-letter word like here it is "MTL"
Secondly, it should be unique for each molecule.
In my case, aldehyde had the unit name "AMN"
Phenol has the unit name "BZN"
But both amine and nitrile got the same name "MTL"
This creates problem later on of repeating units.
One way to overcome the situation is to manually change the unit name for one of the molecule. For example I changed the unit name for the nitrile molecule from "MTL" to "MTN". That takes care of all the problem.
Once your prepin files are ready, next task is to create the frcmod files corresponding to each prepin file.
Use this command:
$AMBERHOME/exe/parmchk -i sustiva.prepin -f prepi -o sustiva.frcmod
Don't forget to replace name "sustiva" by your prepin file name.
Frcmod files carry the information about the improper bond distance, angles, torsions which are not properly defined in the prepin file. So frcmod file help to rectify the original improper values.
Open xleap using the command:
$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
In the xleap window that opens follwoing above command, type
> source leaprc.gaff
(> is xleap prompt, so your command begins from source)
Now load the first molecule say aldehyde by using this command in xleap window:
> loadamberprep aldehyde.prepin
The molecule is loaded, but how will you check if it is right and properly loaded.
For this you need the unit name which you had checked in the prepin file.
I had the unit name AMN for the aldehyde
So I check it using command
> check AMN
You will get following message in the xleap window:
Checking 'AMN'....
Checking parameters for unit 'AMN'.
Checking for bond parameters.
Could not find bond parameter for: c - h4
Checking for angle parameters.
Could not find angle parameter: c3 - c - h4
Could not find angle parameter: h4 - c - o
There are missing parameters.
Unit is OK.
It shows that some of the parameters are not defined and you need to feed in those details. You do so by loading the corresponding frcmod file we generated earlier
So,
> loadamberparams aldehyde.frcmod
You get such a message:
Loading parameters: ./aldehyde.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Once again
> check AMN
This time it should be fine.
Now your molecule is ready for further action. But may be you would like to take a look at the structure.
So:
> edit AMN
A new window showing your structure will appear.
If you have followed instructions properly, you will see proper structure, but if there is some mistake, then probably no window will pop up or else, you will see the structure in dotted form with no bonds formed.
Assuming that you followed the instructions, your structure is ready for next step.
You may close this window showing the structure by clicking on "Unit" followed by "Close".
Don't forget the "Close" click" will be active only with numlock "off".
This finishes loading one molecule.
To load another molecule follow the same procedure in the same xleap window:
> loadamberprep amine.prepin
> check MTL (The unit name for amine was MTL as checked in the prepin file)
> loadamberparams amine.frcmod
> check MTL
> edit MTL
close structure showing window by clicking on Unit --> close.
This way you can prepare as many molecules as you want and load them on the same xleap window.
This way we load xleap with four molecules- aldehyde(AMN), amine(MTL),nitrile(MTN) and phenol(BZN).
(Here nitrile also had MTL unit name mentioned in the prepin file but we changed it to MTN in the prepin file. This avoids duplicacy of the atoms from the 2 molecules)
We now save the parameters of these molecules together in a single lib file
For that we write command:
> saveoff AMN molecule.lib
> saveoff MTL molecule.lib
> saveoff MTN molecule.lib
> saveoff BZN molecule.lib
If you realise now we are using the unit names and not the file names.
So a lib file containing information of 4 molecules is created.This will be useful later.
So now we have say PDB files for four structures - an aldehyde, nitrile, amine and a phenol molecule.
Now, In the first step we generate the prepin files for all these molecules by using:
$AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo prepi -c bcc -s 2
Here the molecules are neutral in nature. If you are working with ionic systems you need to add -nc flag in the end followed by charge of the moelcule.
So, if the moelcule has +1 charge, the command will be:
$AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo prepi -c bcc -s 2 -nc 1
If it is -1, command is:
$AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo prepi -c bcc -s 2 -nc -1
If you have followed earlier preocedure properly then your prepin file should be created in no time.
You can see some lines of a prepin file as an example created for the amine molecule :
----------------------------------
0 0 2
This is a remark line
molecule.res
MTL INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 C1 c3 M 3 2 1 1.540 111.208 180.000 0.14735
5 H12 h1 E 4 3 2 1.071 164.526 20.274 0.04281
6 H13 h1 E 4 3 2 1.069 63.986 -47.277 0.04290
7 H14 h1 E 4 3 2 1.070 62.998 84.283 -0.00841
8 N1 n3 M 4 3 2 1.009 85.966 -161.349 -0.91927
9 H11 hn E 8 4 3 1.011 109.459 -119.526 0.34729
10 H2 hn E 8 4 3 1.011 109.497 0.433 0.34733
-----------------------------
What is worth noting here is the word following line "molecule.res".
The three letters "MTL" defines the unit for the molecule. When you create the prepin file for a molecule in a set of molecules to be cosidered together in a calculation, it is always suggested to open the prepin file and check this unit name.
First of all, it is better if it is a 3-letter word like here it is "MTL"
Secondly, it should be unique for each molecule.
In my case, aldehyde had the unit name "AMN"
Phenol has the unit name "BZN"
But both amine and nitrile got the same name "MTL"
This creates problem later on of repeating units.
One way to overcome the situation is to manually change the unit name for one of the molecule. For example I changed the unit name for the nitrile molecule from "MTL" to "MTN". That takes care of all the problem.
Once your prepin files are ready, next task is to create the frcmod files corresponding to each prepin file.
Use this command:
$AMBERHOME/exe/parmchk -i sustiva.prepin -f prepi -o sustiva.frcmod
Don't forget to replace name "sustiva" by your prepin file name.
Frcmod files carry the information about the improper bond distance, angles, torsions which are not properly defined in the prepin file. So frcmod file help to rectify the original improper values.
Open xleap using the command:
$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
In the xleap window that opens follwoing above command, type
> source leaprc.gaff
(> is xleap prompt, so your command begins from source)
Now load the first molecule say aldehyde by using this command in xleap window:
> loadamberprep aldehyde.prepin
The molecule is loaded, but how will you check if it is right and properly loaded.
For this you need the unit name which you had checked in the prepin file.
I had the unit name AMN for the aldehyde
So I check it using command
> check AMN
You will get following message in the xleap window:
Checking 'AMN'....
Checking parameters for unit 'AMN'.
Checking for bond parameters.
Could not find bond parameter for: c - h4
Checking for angle parameters.
Could not find angle parameter: c3 - c - h4
Could not find angle parameter: h4 - c - o
There are missing parameters.
Unit is OK.
It shows that some of the parameters are not defined and you need to feed in those details. You do so by loading the corresponding frcmod file we generated earlier
So,
> loadamberparams aldehyde.frcmod
You get such a message:
Loading parameters: ./aldehyde.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Once again
> check AMN
This time it should be fine.
Now your molecule is ready for further action. But may be you would like to take a look at the structure.
So:
> edit AMN
A new window showing your structure will appear.
If you have followed instructions properly, you will see proper structure, but if there is some mistake, then probably no window will pop up or else, you will see the structure in dotted form with no bonds formed.
Assuming that you followed the instructions, your structure is ready for next step.
You may close this window showing the structure by clicking on "Unit" followed by "Close".
Don't forget the "Close" click" will be active only with numlock "off".
This finishes loading one molecule.
To load another molecule follow the same procedure in the same xleap window:
> loadamberprep amine.prepin
> check MTL (The unit name for amine was MTL as checked in the prepin file)
> loadamberparams amine.frcmod
> check MTL
> edit MTL
close structure showing window by clicking on Unit --> close.
This way you can prepare as many molecules as you want and load them on the same xleap window.
This way we load xleap with four molecules- aldehyde(AMN), amine(MTL),nitrile(MTN) and phenol(BZN).
(Here nitrile also had MTL unit name mentioned in the prepin file but we changed it to MTN in the prepin file. This avoids duplicacy of the atoms from the 2 molecules)
We now save the parameters of these molecules together in a single lib file
For that we write command:
> saveoff AMN molecule.lib
> saveoff MTL molecule.lib
> saveoff MTN molecule.lib
> saveoff BZN molecule.lib
If you realise now we are using the unit names and not the file names.
So a lib file containing information of 4 molecules is created.This will be useful later.
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