[gmx-users] Problem with pdb2gmx for ATP in PDB file

Raj Badhan r.k.badhan at stud.man.ac.uk
Wed Jan 21 10:53:01 CET 2004

I had the same problem....this is how you fix it:

Put your atps into prodrg, which will assign charges and create a 
gro file for the atp.
The copy and paste this into your protein gro file at the bottom.
BUT, you have to make sure that all the colums are alligned as so:

  462ALA      O1  4469   1.152   3.417   4.013
  462ALA      O2  4470   1.037   3.296   4.189
  463ADP    O2B 4471   4.461   3.235   4.392
  463ADP      PB 4472   4.312   3.238   4.332
  463ADP    O3B 4473   4.215   3.194   4.434
  463ADP    O1B 4474   4.273   3.370   4.280
  463ADP    O3A 4475   4.322   3.141   4.216
  463ADP      PA 4476   4.430   3.112   4.10

Essentially, you simply have to make sure that all the colums align 
downwards and accross, and follow how they align in your protein.
If you dont do this, you will get strange errors when trying to 
solvate your box.
Follow the drug-enzyme tutorial and that will explain in detail how 
to use prodrg and combine gro and itp files into your protein. YOU 
WILL NEED to read this before you can incorporate your files.
Hope that helps

Raj Badhan
Postgraduate researcher
School of Pharmacy and Pharmacetical Science
The University of Manchester
Manchester, UK.

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