Hi Nathan,

Thanks for your reply. 

1. Yes, I have tried to use AMBER force field and converted the pdb2pqr. I was able to dump the charges and radii using this approach. I was wondering if these charges and the resulting hydrogen bonds are going to be accurate even if I do not consider the protonation effects due to the solution pH. 

2. I wanted to convert the individual charges on each atom of my DNA molecule obtained from the above procedure into charge density map. I was using APBS with the input file (abps.in attached with earlier email) and solved the nonlinear PB equation using the above pqr file. The code ran and gave me the potential profile and the ion charge density, however I would like to know how to obtain the charge density of the DNA. I understand that the solver solves the PB equation by converting the individual charges of DNA to charge density map. 

Thanks


On Thu, May 2, 2013 at 9:12 PM, Baker, Nathan <Nathan.Baker@pnnl.gov> wrote:
Hello --

Unfortunately, PROPKA does not currently incorporate DNA titration states.  However, you should be able to assign charges and radii for your molecule using the AMBER force field in PDB2PQR.  Have you tried this?

Thanks,

--
Nathan Baker
Pacific Northwest National Laboratory
Phone: +1-509-375-3997
http://nabaker.me

From: nandigana vishal <nandiganavishal@gmail.com<mailto:nandiganavishal@gmail.com>>
Date: Wednesday, May 1, 2013 5:12 PM
To: APBS-USERS mailing list <apbs-users@googlegroups.com<mailto:apbs-users@googlegroups.com>>
Subject: [apbs-users] how to get the charge density of input DNA.pdb file

Hi all,

I am relatively new to using APBS and pdb2pqr. I have created a simple ssDNA poly(dA)_40 using 3D DART software (the pdb file is attached) and had calculated the local charge on each atom using pdb2pqr.

1. If I understand correctly, propKa would include the protonation effects due to the pH of the solution and hence, would add hydrogen bonds to the DNA and alter the partial charges of the hydrogen suitably.

When I tried to convert the pdb2pqr of my DNA, I was able to convert them when the propKa option was not checked. However, the simulation failed when the propKa option was selected. Please let me know what caused this failure.

2. I wanted to convert the individual charges on each atom of my DNA molecule into charge density map. I was using APBS with the input file (abps.in attached with this email) and solved the nonlinear PB equation using the above pqr file. The code ran and gave me the potential profile and the ion charge density, however I would like to know how to obtain the charge density of the DNA. I understand that the solver solves the PB equation by converting the individual charges of DNA to charge density map.

Please let me know the answers to the above queries.

Thanks.

Regards,
Vishal



--
Regards

Vishal Nandigana
PhD Student, Mechanical Engineering
University of Illinois at Urbana Champaign,
Beckman Institute for Advanced Sciences
Room no - 3213,
Illinois 61820,
U.S.A.