Re: [Apbs-users] psf from pqr file

[Nathan B. <ba...@bi...>]

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
>
>
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-- 
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/