[gmx-users] Question about DNA simulation

[Maik Goette]

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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>