Thread: [Apbs-users] how to consider the effect of membrane
Biomolecular electrostatics software
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From: Xiaoqing W. <kit...@12...> - 2005-06-15 03:33:10
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Hi, I have a systerm of protein+membrane+water+ion. I want to calculate the electrostatic potential of the protein. When I use the script file "pdb2pqr.py" ,only protein and ions can be identified. How can I consider the effect of membrane? Any tips would be greatly appreciated! Sincerely, Xiaoqing |
From: Xiaoqing W. <ap...@12...> - 2005-06-14 15:39:09
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Hi, I have a systerm of protein+membrane+water+ion. I want to calculate the electrostatic potential of the protein. When I use the script file "pdb2pqr.py" ,only protein and ions can be identified. How can I consider the effect of membrane? Any tips would be greatly appreciated! |
From: Nathan B. <ba...@bi...> - 2005-06-15 13:48:55
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PDB2PQR will currently only recognize standard amino acid residues in the AMBER, CHARMM, and PARSE force field as well as a few ions, etc. You'll need to load the lipid and water parameters by using "READ PARM" (see http://agave.wustl.edu/apbs/doc/html/user-guide/x645.html#read) or modifying the PQR file with awk or something similar. Good luck, Nathan --- Xiaoqing Wang <kit...@12...> wrote: > Hi, > > I have a systerm of protein+membrane+water+ion. I want to calculate > the electrostatic potential of the protein. When I use the script file > "pdb2pqr.py" ,only protein and ions can be identified. How can I > consider the effect of membrane? > > Any tips would be greatly appreciated! > > Sincerely, > Xiaoqing > > > > _______________________________________________ > apbs-users mailing list > apb...@ch... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Washington University in St. Louis http://cholla.wustl.edu |
From: Xiaoqing W. <kit...@12...> - 2005-06-15 14:53:15
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Hi Nathan, Thank you very much! I have another question. How to obtain the atomic radius of lipid(POPE) and water(TIP3)? I have the .psf file of the systerm, but it only contains atomic charges. Any tips would be greatly appreciated! Sincerely, Xiaoqing > PDB2PQR will currently only recognize standard amino acid residues in the > AMBER, CHARMM, and PARSE force field as well as a few ions, etc. You'll need > to load the lipid and water parameters by using "READ PARM" (see > http://agave.wustl.edu/apbs/doc/html/user-guide/x645.html#read) or modifying > the PQR file with awk or something similar. > > Good luck, > > Nathan > > --- Xiaoqing Wang <kit...@12...> wrote: > > > Hi, > > > > I have a systerm of protein+membrane+water+ion. I want to calculate > > the electrostatic potential of the protein. When I use the script file > > "pdb2pqr.py" ,only protein and ions can be identified. How can I > > consider the effect of membrane? > > > > Any tips would be greatly appreciated! > > > > Sincerely, > > Xiaoqing > > > > > > > > _______________________________________________ > > apbs-users mailing list > > apb...@ch... > > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > > > > > > -- > Assistant Professor, Dept. of Biochemistry and Molecular Biophysics > Washington University in St. Louis > http://cholla.wustl.edu > _______________________________________________ > apbs-users mailing list > apb...@ch... > http://cholla.wustl.edu/mailman/listinfo/apbs-users |