David
I think, I should not contradict to one of the developers, but if your
statement is true:
1. Where, in fact, are the masses coming from (the masses in the amberFF
port can only be found in the atp, as far as I know)?
2. Why does GROMACS complain about missing atoms in the atp-file, if I
add a new atom type to the nb-section?
Just out of curiosity...
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
David van der Spoel wrote:
Maik Goette wrote:
Because it is?
The masses are defined in the .atp file. I dont't know how GROMACS
handles the stuff, but that is sufficiant....Maybe Eric was a bit lazy...
Why do you care for that...?
atp file is never used...
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
bo yang wrote:
Hello,
I have a question regarding DNA simulation.
I have the amber99 package.
Can anyone give me an explanation why all the masses in the
ffamberXXnb.itp are 0?
Thank you very much!
Bo
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