Re: [Apbs-users] problem with APBS calculation

[David G. <sd...@gm...>]

Hi Changrong,

   I think PyMOL is referring to the atoms in GDD. From the PDB2PQR  
server:

REMARK   5 WARNING: PDB2PQR was unable to assign charges
REMARK   5          to the following atoms (omitted below):
REMARK   5              2681 N2 in GDD 2567
REMARK   5              2682 C2 in GDD 2567
REMARK   5              2683 N1 in GDD 2567
REMARK   5              2684 N3 in GDD 2567
REMARK   5              2685 C4 in GDD 2567
REMARK   5              2686 C5 in GDD 2567
REMARK   5              2687 C6 in GDD 2567
REMARK   5              2688 O6 in GDD 2567
...

   The PDB2PQR server silently strips these atoms out. Which probably  
isn't what you want. So you may need to assign the charges and radii  
yourself (after adding the atoms back in). I'm not certain if you can  
append charges and radii for select atoms in PDB2PQR directly.   
Similarly, I'm not certain where PyMOL gets its charges and radii for  
PDB files from.

   Regards,

Dave


On Dec 14, 2008, at 11:50 AM, Changrong Ge wrote:

> Hej,
>      met some problem when I calculated the surface potential for  
> the enclosed protein by APBS in Pymol. something like"program could  
> not assign charge parameters for 101 atoms ", could anybody solve  
> this for me?
>      thanks
>      Changrong
> < 
> 2GEJ 
> .pdb 
> > 
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David W. Gohara, Ph.D.
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Washington University School of Medicine
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