Thread: [Apbs-users] psf from pqr file
Biomolecular electrostatics software
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From: Abhishek S. R. <abh...@um...> - 2009-04-21 21:10:58
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Hi, I am in need of running molecular dynamics simulation for different protonation states of 1cwp.pdb (CCMV) over the range 4 to 7. One way of making the .psf file will be to alias the residues with protonation states given in the topology file and use guesscoord to add protons. But this is completely independent of the local structure of the protein. I was thinking of making a .pqr file ( using pdb2pqr that has debumping algorithm and H-bond optimization, that makes protonation sensitive to the protein structure) and make a .psf out of it. This means aliasing for a large number of the added protons every time I do this, for different systems. Please let me know if there is an efficient way of doing this. Thanks Abhishek |
From: Nathan B. <ba...@bi...> - 2009-04-22 11:52:39
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Hello -- Unfortunately, I don't know of any easy way to do this. However, the PQR format isn't that different from the PDB format, so it seems likely that you could adapt existing PSF/PDB-handing routines to your task. Good luck! -- Nathan On Tue, Apr 21, 2009 at 4:04 PM, Abhishek Singha Roy <abh...@um...>wrote: > Hi, > I am in need of running molecular dynamics simulation for different > protonation states of 1cwp.pdb (CCMV) over the range 4 to 7. > > One way of making the .psf file will be to alias the residues with > protonation states given in the topology file and use guesscoord to add > protons. But this is completely independent of the local structure of the > protein. > > I was thinking of making a .pqr file ( using pdb2pqr that has debumping > algorithm and H-bond optimization, that makes protonation sensitive to the > protein structure) and make a .psf out of it. This means aliasing for a > large number of the added protons every time I do this, for different > systems. > > Please let me know if there is an efficient way of doing this. > Thanks > Abhishek > > > ------------------------------------------------------------------------------ > Stay on top of everything new and different, both inside and > around Java (TM) technology - register by April 22, and save > $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. > 300 plus technical and hands-on sessions. Register today. > Use priority code J9JMT32. http://p.sf.net/sfu/p > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |