Sometimes you totally fail to go ahead with the prepin and frcmod files you have generated from the newly generated PDB file even after you follow the procedure given in previous two posts. And you keep wondering?
In such a case you need a more detailed procedure.
First take a look at the pdb file.
For example:
Here is one such pdb file generated from the gabedit that troubled me for some time.
---------------
HEADER PROTEIN
COMPND UNNAMED
AUTHOR GENERATED BY GABEDIT 2.3.8 at Tue Jul 26 16:53:48 2011
ATOM 1 C C 1 -2.907 -0.997 -0.385 1.00 300.00 C 0.0000
ATOM 2 N N 1 -2.060 -0.981 -1.189 1.00 300.00 N 0.0000
ATOM 3 C C 1 -1.026 -0.973 -2.172 1.00 300.00 C 0.0000
ATOM 4 H H 1 -0.409 -1.865 -2.044 1.00 300.00 H 0.0000
ATOM 5 H H 1 -0.409 -0.082 -2.038 1.00 300.00 H 0.0000
ATOM 6 H H 1 -1.476 -0.977 -3.165 1.00 300.00 H 0.0000
CONECT 1 2
CONECT 2 1 3
CONECT 3 2 4 5 6
CONECT 4 3
CONECT 5 3
CONECT 6 3
MASTER 0 0 0 0 0 0 0 0 6 0 6 0
END
---------------------
When you generate a prepin file for this, it appears something like this:
------------------------------
0 0 2
This is a remark line
molecule.res
C 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 C c1 M 3 2 1 1.540 111.208 180.000 0.43498
5 N n1 M 4 3 2 1.168 136.486 91.140 -0.85143
6 C1 c3 M 5 4 3 1.427 179.534 -85.467 0.25973
7 H h1 E 6 5 4 1.092 108.912 -35.443 0.05222
8 H1 h1 E 6 5 4 1.092 109.239 -154.928 0.05225
9 H2 h1 E 6 5 4 1.090 109.171 84.306 0.05225
LOOP
IMPROPER
DONE
STOP
---------------------------------------
The unit name is bit odd. Just a "C".
It gives problem ahead where it fails to read and understand the unit name properly and therefore the atoms name and type in it. And you end up with some error.
So to move ahead, what you do is you replace the entries in the fourth column of the PDB file (which are shown in bold) by a common three letter word. Here I replace all of them by word "TSN". My PDB file now looks like:
----------------
HEADER PROTEIN
COMPND UNNAMED
AUTHOR GENERATED BY GABEDIT 2.3.8 at Tue Jul 26 16:53:48 2011
ATOM 1 C TSN 1 -2.907 -0.997 -0.385 1.00 300.00 C 0.0000
ATOM 2 N TSN 1 -2.060 -0.981 -1.189 1.00 300.00 N 0.0000
ATOM 3 C TSN 1 -1.026 -0.973 -2.172 1.00 300.00 C 0.0000
ATOM 4 H TSN 1 -0.409 -1.865 -2.044 1.00 300.00 H 0.0000
ATOM 5 H TSN 1 -0.409 -0.082 -2.038 1.00 300.00 H 0.0000
ATOM 6 H TSN 1 -1.476 -0.977 -3.165 1.00 300.00 H 0.0000
CONECT 1 2
CONECT 2 1 3
CONECT 3 2 4 5 6
CONECT 4 3
CONECT 5 3
CONECT 6 3
MASTER 0 0 0 0 0 0 0 0 6 0 6 0
END
-----------------
And when you generate the prepin file it appears like this:
--------------------
0 0 2
This is a remark line
molecule.res
TSN 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 C c1 M 3 2 1 1.540 111.208 180.000 0.43498
5 N n1 M 4 3 2 1.168 136.486 91.140 -0.85143
6 C1 c3 M 5 4 3 1.427 179.534 -85.467 0.25973
7 H h1 E 6 5 4 1.092 108.912 -35.443 0.05222
8 H1 h1 E 6 5 4 1.092 109.239 -154.928 0.05225
9 H2 h1 E 6 5 4 1.090 109.171 84.306 0.05225
LOOP
IMPROPER
DONE
STOP
---------------------
Check the change in the unit name. "TSN" here.
Once I created the prepin file followed by frcmod file, load the prepin file in xleap followed by frcmod. check the unit and save the unit as a pdb file using:
> savepdb TSN new_molecule.pdb
This will save the molecule in pdb format that is acceptable to the the xleap.
So the new_molecule.pdb file looks like:
-------------------------
ATOM 1 C TSN 1 3.537 1.423 -0.000 1.00 0.00
ATOM 2 N TSN 1 4.384 1.440 -0.804 1.00 0.00
ATOM 3 C1 TSN 1 5.418 1.450 -1.787 1.00 0.00
ATOM 4 H TSN 1 6.037 0.560 -1.659 1.00 0.00
ATOM 5 H1 TSN 1 6.033 2.343 -1.653 1.00 0.00
ATOM 6 H2 TSN 1 4.968 1.446 -2.780 1.00 0.00
TER
END
--------------------------
Use this pdb file to create prepin and frcmod file. Create the prepin and frcmod files for all the molecules you are considering. Load them in xleap and create the common lib file as explained in earlier post.
Now why do we do all this jugglery?
One reason: it takes care of the unit name, which is a bottle neck while dealing with xleap.
Second reason: it brings the pdb files of all the molecules in one common format which is generally acceptable to xleap.
Third reason: We in coming steps need to create a single common pdb file including all the molecules. This single common pdb file should match the details stored in the combined lib file we create.
If that does not happen all efforts taken till now go vain and we might need to start right from scratch.
So in summary:
Generate a PDB file manually from gabedit
Check the file and change the fourth column by a common three letter word in each row.
Create the prepin and frcmod file for the modified pdb file
load it in xleap and save the unit (the three letter word we changed in PDB file) as a new pdb file.
Use this new pdb file to create the prepin and frcmod files.
Follow the procedure for all the molecules you are considering.
load them all in the xleap and save them in a single common lib file.
The new lib file created is the one to be used further.
In such a case you need a more detailed procedure.
First take a look at the pdb file.
For example:
Here is one such pdb file generated from the gabedit that troubled me for some time.
---------------
HEADER PROTEIN
COMPND UNNAMED
AUTHOR GENERATED BY GABEDIT 2.3.8 at Tue Jul 26 16:53:48 2011
ATOM 1 C C 1 -2.907 -0.997 -0.385 1.00 300.00 C 0.0000
ATOM 2 N N 1 -2.060 -0.981 -1.189 1.00 300.00 N 0.0000
ATOM 3 C C 1 -1.026 -0.973 -2.172 1.00 300.00 C 0.0000
ATOM 4 H H 1 -0.409 -1.865 -2.044 1.00 300.00 H 0.0000
ATOM 5 H H 1 -0.409 -0.082 -2.038 1.00 300.00 H 0.0000
ATOM 6 H H 1 -1.476 -0.977 -3.165 1.00 300.00 H 0.0000
CONECT 1 2
CONECT 2 1 3
CONECT 3 2 4 5 6
CONECT 4 3
CONECT 5 3
CONECT 6 3
MASTER 0 0 0 0 0 0 0 0 6 0 6 0
END
---------------------
When you generate a prepin file for this, it appears something like this:
------------------------------
0 0 2
This is a remark line
molecule.res
C 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 C c1 M 3 2 1 1.540 111.208 180.000 0.43498
5 N n1 M 4 3 2 1.168 136.486 91.140 -0.85143
6 C1 c3 M 5 4 3 1.427 179.534 -85.467 0.25973
7 H h1 E 6 5 4 1.092 108.912 -35.443 0.05222
8 H1 h1 E 6 5 4 1.092 109.239 -154.928 0.05225
9 H2 h1 E 6 5 4 1.090 109.171 84.306 0.05225
LOOP
IMPROPER
DONE
STOP
---------------------------------------
The unit name is bit odd. Just a "C".
It gives problem ahead where it fails to read and understand the unit name properly and therefore the atoms name and type in it. And you end up with some error.
So to move ahead, what you do is you replace the entries in the fourth column of the PDB file (which are shown in bold) by a common three letter word. Here I replace all of them by word "TSN". My PDB file now looks like:
----------------
HEADER PROTEIN
COMPND UNNAMED
AUTHOR GENERATED BY GABEDIT 2.3.8 at Tue Jul 26 16:53:48 2011
ATOM 1 C TSN 1 -2.907 -0.997 -0.385 1.00 300.00 C 0.0000
ATOM 2 N TSN 1 -2.060 -0.981 -1.189 1.00 300.00 N 0.0000
ATOM 3 C TSN 1 -1.026 -0.973 -2.172 1.00 300.00 C 0.0000
ATOM 4 H TSN 1 -0.409 -1.865 -2.044 1.00 300.00 H 0.0000
ATOM 5 H TSN 1 -0.409 -0.082 -2.038 1.00 300.00 H 0.0000
ATOM 6 H TSN 1 -1.476 -0.977 -3.165 1.00 300.00 H 0.0000
CONECT 1 2
CONECT 2 1 3
CONECT 3 2 4 5 6
CONECT 4 3
CONECT 5 3
CONECT 6 3
MASTER 0 0 0 0 0 0 0 0 6 0 6 0
END
-----------------
And when you generate the prepin file it appears like this:
--------------------
0 0 2
This is a remark line
molecule.res
TSN 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 C c1 M 3 2 1 1.540 111.208 180.000 0.43498
5 N n1 M 4 3 2 1.168 136.486 91.140 -0.85143
6 C1 c3 M 5 4 3 1.427 179.534 -85.467 0.25973
7 H h1 E 6 5 4 1.092 108.912 -35.443 0.05222
8 H1 h1 E 6 5 4 1.092 109.239 -154.928 0.05225
9 H2 h1 E 6 5 4 1.090 109.171 84.306 0.05225
LOOP
IMPROPER
DONE
STOP
---------------------
Check the change in the unit name. "TSN" here.
Once I created the prepin file followed by frcmod file, load the prepin file in xleap followed by frcmod. check the unit and save the unit as a pdb file using:
> savepdb TSN new_molecule.pdb
This will save the molecule in pdb format that is acceptable to the the xleap.
So the new_molecule.pdb file looks like:
-------------------------
ATOM 1 C TSN 1 3.537 1.423 -0.000 1.00 0.00
ATOM 2 N TSN 1 4.384 1.440 -0.804 1.00 0.00
ATOM 3 C1 TSN 1 5.418 1.450 -1.787 1.00 0.00
ATOM 4 H TSN 1 6.037 0.560 -1.659 1.00 0.00
ATOM 5 H1 TSN 1 6.033 2.343 -1.653 1.00 0.00
ATOM 6 H2 TSN 1 4.968 1.446 -2.780 1.00 0.00
TER
END
--------------------------
Use this pdb file to create prepin and frcmod file. Create the prepin and frcmod files for all the molecules you are considering. Load them in xleap and create the common lib file as explained in earlier post.
Now why do we do all this jugglery?
One reason: it takes care of the unit name, which is a bottle neck while dealing with xleap.
Second reason: it brings the pdb files of all the molecules in one common format which is generally acceptable to xleap.
Third reason: We in coming steps need to create a single common pdb file including all the molecules. This single common pdb file should match the details stored in the combined lib file we create.
If that does not happen all efforts taken till now go vain and we might need to start right from scratch.
So in summary:
Generate a PDB file manually from gabedit
Check the file and change the fourth column by a common three letter word in each row.
Create the prepin and frcmod file for the modified pdb file
load it in xleap and save the unit (the three letter word we changed in PDB file) as a new pdb file.
Use this new pdb file to create the prepin and frcmod files.
Follow the procedure for all the molecules you are considering.
load them all in the xleap and save them in a single common lib file.
The new lib file created is the one to be used further.
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