[gmx-users] protein drug tutorial

[Anton Feenstra]

John Kerrigan wrote:
> 
> chandran-
> 
> I trust you added your drug coordinates to the end of your overall protein
> gro file.  There are a couple of edits that you must perform to satisfy
> grompp.
> 
> 1.  Re-number the atoms in the drug portion you added so they
> continue from where the protein left off.  In other words, the # sequence
> cannot be interrupted then restarted again (1, 2, 3, ... 1, 2, 3 is not
> allowed).  There cannot be any numbers missing in the sequence, either.
> 2.  Revise the total number of atoms at the beginning of the file so it
> reflects the new total (accounting for the # of drug atoms).
> 3.  You may need to revise the residue # so that it is consecutive with
> the protein as well.  

Residue and atom numbers in the .gro file are irrelevant, you do not need
to adjust them. The atom/residue numbers also do not need to match those
in your .top/.itp files. (Numbering in the .top/.itp files themselves is
another matter.) So, when combining two .gro files you only need to make
sure you update the number of atoms counter at the top, remove the box line
from bottom of the first .gro file and remove the atom number and title
from the top of the second .gro file.

Alternatively, you can first convert both .gro files to .pdb (use
editconf -f file1.gro -o file1.pdb), then 'cat' both .pdb files
into one (and convert that back to .gro, if you want). This is easily
automated in a script:

editconf -f file1.gro -o file1.pdb
editconf -f file2.gro -o file2.pdb
cat file1.pdb file2.pdb > file_all.pdb
editconf -f file_all.pdb -o file_all.gro
Note, that in this case the box from file1.gro will be used.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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