[gmx-users] Problem with pdb2gmx for ATP in PDB file
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
School of Pharmacy and Pharmacetical Science
The University of Manchester
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