[gmx-users] opls to gromos conversion

David spoel at xray.bmc.uu.se
Tue Jul 26 12:36:02 CEST 2005

On Tue, 2005-07-26 at 10:49 +0200, Minami Mo wrote:
> Dear gromacs users,
> I would like to use the output from a simulation using OPLS ff to run
> in GROMOS ff. Does anyone know if there is a way of doing it, while
> keeping all the coordinates (including water)? I tried feeding the
> output pdb (from the first simulation) to pdb2gmx and it prompted out
> errors saying that it couldn't recognize some H, and it works only if
> I remove all hydrogens.
How about mdrun -rerun?

You will have to strip the non-polar hydrogens from the protein using

> Thanks for all inputs.
> Minami
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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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