VMD-L Mailing List

From: Mamoru Yamanishi (myamanishi3_at_unl.edu)
Date: Wed Dec 07 2005 - 14:18:48 CST

Hello,

> I try to run the APBS plugin. I load a .gro file and the I make a selection
> of only the protein. Then I try to run apbs and the following message
> appears: molecule is uncharge procede??? (YES) (NO) if I choose yes this
> message appears in the vmd console apbsrun: warning, can't find parameter
> file. Then I stop the run What parameter file I need??? How to input the
> parameters???

I had a same problem with *.PDB file. The following is my current
understanding.

APBS requires CHARGE and RADIUS information (in addition xyz
coordinate) for each atom. APBS uses PQR format file which is
generated by VMD. Unfortunately, such file lacks CHARGE
information, which is always 0.00.

Probably, your case is the same.

To add CHARGE information, the best way is to generate PQR
format file by yourself. Please look up

        http://pdb2pqr.sourceforge.net/

I used a web service.

I do not know how to convert GRO file to PQR directly. 

-- 
Mamoru Yamanishi, Ph.D. <myamanishi3_at_unl.edu>
Research Assistant Professor
Dr. Banerjee's Lab., Biochemistry Department
University of Nebraska-Lincoln