Hi Davide,

On Thu, Sep 24, 2009 at 5:57 PM, Davide Mercadante <dmer018@aucklanduni.ac.nz> wrote:
Dear APBS users,

I have the following problem. I need to generate the .pqr file of an oligosaccharidic chain for further electrostatic potential calculations using APBS. Obviously I have difficulties because whatever is the forcefield used pdb2pqr gives the error "No Heavy ATOMS Found!". This I think happens because there are no parameters for the atoms of my oligosaccharide.
If I use the flag --clean the error disappears and I am able to generate the .pqr file but the column relative to the charges report 0.000 for each atoms (I suppose because those atoms are not optimized and not recognized).

Sorry but PDB2PQR is saying there are no amino acids or nucleic acids in your pdb. As a result, PDB2PQR will be unable to proceed with the designed routines (adding limited number of missing heavy atoms, placing missing hydrogens, optimizing hydrogen bonds, assigning charge and radius parameters, etc.). If this structure is not a protein, PDB2PQR will hardly be useful in here. However, if you have the parameters for your atoms, you can try modifying the data file(s) and using --assign-only option of PDB2PQR.
 
My questions are the following:

1) If I would to modify the parameters files of the forcefield that I want to use for generating the .pqr file what are the files that I have to modify? Which is the directory where I found the files in pdb2pqr code? (I found the files .DAT of the forcefields in the directory /pdb2pqr/dat/ are those that I need to modify?)


Depending on the force field you use, e.g., if you use AMBER force field, then dat/AMBER.DAT is the file you want to modify.
 
2) Which are the parameters that I have to report in the .DAT file (I see first column is residue's name, 2nd column is atom type, 3rd column ?, 4th column ?, 5th comlumn atom name I guess)...


3rd column is charge, 4th column is radius, 5th column is group name.
 
3) where I can get the parameters for these atoms?

AMBER and CHARMM mailing lists, related literature should be good places to start.

Thanks,

Yong

 

Thanks infinitely in advance for your help or suggestions.

Cheers,
Davide

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--
Yong Huang, D.Sc.

Center for Computational Biology
Washington University School of Medicine