On Apr 11, 2013 11:51 PM, "Laura Kingsley" wrote:
>
> So if I'm understanding you correctly in the .rtp file under
>
> [ HEME ]
> [ dihedrals ]
>
> I should change:
>HP42 CBD CGD O1D
>HP42 CBD CGD O2D
> ...
>
> to
>
>HP42 CBD CGD O1D30.65270 1.95811 0.00
So if I'm understanding you correctly in the .rtp file under
[ HEME ]
[ dihedrals ]
I should change:
HP42 CBD CGD O1D
HP42 CBD CGD O2D
...
to
HP42 CBD CGD O1D30.65270 1.95811 0.0 -2.61082
0.0 0.0
HP42 CBD CGD O2D30.65270
On Thu, Apr 11, 2013 at 11:14 PM, Laura Kingsley wrote:
> Hi Mark,
>
> We'd like to use the Ryckaert-Bellemans dihedral types. Does 3 not work in
> the new version?
Sorry, I was thinking of 4 and 9, which are basically interchangeable. The
default for AMBER did change to 9 at some point (see top
Hi Mark,
We'd like to use the Ryckaert-Bellemans dihedral types. Does 3 not work
in the new version? Also, I took out the #define lines and replaced them
with the actual atomtypes, because that didn't seem to work when I
initially tried to add just the #define lines to the ffbonded.itp file.
Type 9 was added at some point to GROMACS to make coping with AMBER and
CHARMM easier. So you should just change your #defines from 3 to 9. See
table in chapter 5. Or you could just leave your solution in the same form
as you did for the 4.0.x GROMACS.
Mark
On Thu, Apr 11, 2013 at 10:36 PM, Laur
Hello Gromacs Users,
I am trying to update the contents of the top folder. I have parameters
for a HEME residue that worked in gromacs 4.0.7, and we're now trying to
update to gromacs 4.6.1 (long overdue), and need to migrate the
parameters over to the new version.
I have done the following
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