Note that you could add a few protein residues (e.g., a small alpha helix) away from the ligand to circumvent this problem.

Thanks,

Nathan

On Mon, Dec 22, 2008 at 9:26 AM, Yong Huang <yhuang01@gmail.com> wrote:
Hello,

For PDB2PQR to run properly on your pdb, "standard residues" are expected in this pdb file. In other words, the lines beginning with "ATOM" are missing from your attached pdb file. There are only non-standard HETATM and CONECT records in it (and REMARK, of course), and that's why PDB2PQR sent out the "No heavy atoms found" message.

Thanks,

Yong


2008/12/22 有盼 缪 <youpan20032003@yahoo.com.cn>
dear users:
I want to get the PQR file of the small molecule DRGFIN.PDB in the enclosure to run apbs,
but when I run PDB2PQR , I always get the error massege below:
   no heavy atoms found.
I want to know the reason , and how to solve it.
Waiting for your help ,
Thank you very much!


好玩贺卡等你发,邮箱贺卡全新上线!

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Yong Huang, D.Sc.

Center for Computational Biology
Washington University School of Medicine

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Web: http://cholla.wustl.edu/