[gmx-users] Generating coordinates for non-protein molecules

David spoel at xray.bmc.uu.se
Sat Aug 6 08:57:10 CEST 2005

On Fri, 2005-08-05 at 16:39 -0400, deepa rajamani wrote:
> Hi,
> I am trying to run MD simulations of protein with a small molecule system.
> How can I include the coordinates of small molecules in the .gro file
> How can I generate coordinates for the polar hydrogens which are not 
> present in the small molecule pdb file.
> I have used PRODRG to make the topology files for the small molecule.
prodrg also gives you coordinates.

> I also tried approximating the coordinates of the small molecule and 
> appending it to the protein.gro file. The only problem is that it does not 
> have the polar hydrogens in it and the coordinates are approximated.
> Thanks for any suggestions
> Deepa
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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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