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Electrostatics / apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation
http://www.poissonboltzmann.org/
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PDB with 2 ZN+ ligands #524

Closed skigirl618 closed 5 years ago

skigirl618 commented 5 years ago

Hello,

     I have a PDB file that contains 2 added ZN+ ligands that I need to look at the electrostatic potential. In order to use APBS I tried to run the file through PDB2PQR but I got an error message. I do not know if I need to use different settings, etc. so I was looking for some advice. I have attached my PDB below.

Refined C1 domain with both zincs copy.txt

kozlac commented 5 years ago

Hello @skigirl618! To include ligands in the calculations you need to provide their corresponding mol2 files/ Please look at this example and let me know if you get stuck. Thanks!

skigirl618 commented 5 years ago

Hello Juan,

     I am working with homology models and I do not have mol2 files so how do I obtain those? In addition, it seems that there is only 1 upload slot of a mol2 file on the PDB2PQR server, but I have 2 ligands (so I assume I would have 2 files). How do I work around that? Thanks for the help!

Sincerely, Abbey

On Jun 12, 2019, at 6:02 PM, Juan notifications@github.com wrote:

Hello @skigirl618 https://github.com/skigirl618! To include ligands in the calculations you need to provide their corresponding mol2 files/ Please look at this example https://apbs-pdb2pqr.readthedocs.io/en/latest/examples/parameterizing-ligands.html and let me know if you get stuck. Thanks!

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kozlac commented 5 years ago

@skigirl618, unfortunately, we only support one ligand at the moment. To get the mol2 file you can go to http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg/ and copy paste the relevant pdb entries.