Re: [Apbs-users] electrostatics of a small molecule an calculation of desolvation energy

[Daniel A. W. <da...@br...>]

Hi Rosemary,

The PDB2PQR server was hanging for several days for me last week too, and it turned out it was because my mol2 was missing 2 lines- I had saved a small molecule as a .mol2 in Spartan, and it left out the following at the end:

@<TRIPOS>SUBSTRUCTURE
  1  DRG    1  

When I created the mol2 with the PRODRG server and tried that on PDB2PQR, it returned the pqr immediately.

-Daniel

----- Original Message -----
From: "Rosemary Harrison" <r.h...@im...>
To: apb...@li...
Sent: Sunday, December 21, 2008 5:10:52 AM GMT -06:00 US/Canada Central
Subject: [Apbs-users] electrostatics of a small molecule an calculation of desolvation energy

> Hi APBS users,
>
> I am looking for some advice on electrostatic maps of small molecules.
>
> What is the best program for this?
>
> Is there anyway I can calculate the desolvation energy at the same  
> time?
>
> I have tried to create a PQR file for APBS (through PDB2PQR) with  
> the pdb of the small molecule (and the mol2 file) - but it seems to  
> be hanging after 4 days.
>
> Any help would be greatly appreciated
>
> Rose Harrison

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