[gmx-users] v3.2.1 to v3.3 problems

[David van der Spoel]

Dave Segala wrote:
> Hi all,
> 
> I am using the opls-aa force field to simulate my molecule. I have files
> which ran correctly on version 3.2.1 and are not running on version 3.3.
> When I use the command pdb2gmx I encounter many errors:
> 1. wrong input on ffolpsaa.hdb file
>      2 7 OW
> when I change to 2 7 HW OW, it works.
> 
> 2. in the -c and -n .tdb files there are only supposed to be 4 entries in
> [replace] and in [add] 3 entries on the second line.
> 
> After changing only these files an atom is not found where combining the
> .tdb and .rtp files to create the .top file.
> 
> Does anyone have any suggestions on how to fix these problem or where to
> look.
> 
> Cheers,
> Dave
> 
the format of the hdb file has changed, and new files are provided. the 
same goes for the tdb files: the name of the atom to replace has to be 
added. If you have added stuff to your old files, you can by comparing 
the standard 3.2 and 3.3 files, deduce how to make your changes work 
with 3.3.

-- 
David.
________________________________________________________________________
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://folding.bmc.uu.se
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