Hello,

Sorry but it looks like there are no amino acids or nucleic acids in your pdb, as a result, PDB2PQR will be unable to perform its designed routines: adding limited number of missing heavy atoms, placing missing hydrogens, optimizing hydrogen-bond network, debumping atoms, assigning charge and radius parameters from different forcefields, etc. In this case, PDB2PQR will not be very useful to your analysis.

Sorry,

Yong


2009/9/8 Fernando Zamarreño <fernandozamarreno@gmail.com>
Perhaps the file is too heavy??

2009/9/8 Yong Huang <yhuang01@gmail.com>

Hello,

Could you send us an example with your pdb file in it, so that we can determine the true nature of this issue?

Thanks,

Yong


2009/9/8 Fernando Zamarreño <fernandozamarreno@gmail.com>
Hi!
I am trying to generate a .pqr file from a cellular membrane .pdb file with the pdb2pqr server. It seems that the server will not be able to do it. Is there another way to do it?
Thanks!
Fernando.
 

--

Bioq. Fernando Zamarreño
Grupo de Biofísica
Dpto. de Física
Univerisdad Nacional del Sur
Avda. Alem 1253  -  (8000) Bahia Blanca

Tel.: +54 (291) 4595101 Ext 2805
Fax:+54 (291) 4595142
http://www.uns.edu.ar
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--
Yong Huang, D.Sc.

Center for Computational Biology
Washington University School of Medicine



--

Bioq. Fernando Zamarreño
Grupo de Biofísica
Dpto. de Física
Univerisdad Nacional del Sur
Avda. Alem 1253  -  (8000) Bahia Blanca

Tel.: +54 (291) 4595101 Ext 2805
Fax:+54 (291) 4595142
http://www.uns.edu.ar
-------------------------------------------------------



--
Yong Huang, D.Sc.

Center for Computational Biology
Washington University School of Medicine