[gmx-users] Generating a PQR file
David van der Spoel
spoel at xray.bmc.uu.se
Sat Jul 8 10:34:10 CEST 2006
On Fri, 7 Jul 2006, Bob Johnson wrote:
>I would like to create a PQR file (basically a PDB file but with charges in
>B-field and radii in occupancy field). However, there doesn't seem to be any
>straightforward way to do this.
>I noticed that this could be done with editconf, however this is difficult given
>the way I have my topologies set up. I have a separate topology (.itp) for each
>molecule in my system (dna, water, counterions, etc.). Thus, the atom numbers
>in these files are not unique. Thus, there is no good way of feeding in the
>charges to editconf by listing the charge for each atom number. Is there a way
>to extract this information from a .tpr file?
don't you have one cmoplete tpr file for the whole system?
then editconf will do the trick.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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