Hi
By modifying parm99.dat and using xleap, I got a parameter file with 10_12
information in it. It seems to be an improvement over my manual
modifications because I missed some numbers. However, when run with
sander in Amber9, it still does not work (all vdw energies are 0). Next I
will try falling back to Amber8. I really need the 10_12 potential to
decrease linear expansion. If anyone knows where in the code I can modify
the vdw potential by using r^10 instead of r^6, I would appreciate it.
Thanks
Andrew Petersen
> Dr Case
> My system is simple (methane). I thought it would be easier to modify my
> 6_12 parameter files. So there are 4 nonbon interactions, H..H, H..C,
> C..H, C..C, with ICO indices 1, 2, 2, and 3. So I changed NPHB from 0 to
> 4,
> made the ICO indices negative, and put A & B values in the hbond_coef
> positions. But it does not work, giving me 0 vdw energies. I will try
> what you suggest.
> AP
>> On Mon, Feb 08, 2010, aapeters.ncsu.edu wrote:
>>>
>>> I'm trying to use the 10-12 potential with Langevin dynamics with
>>> serial
>>> sander in Amber9.
>>>
>>> I created a 10-12 prm file by manually editing one of my 12-6 parameter
>>> files.
>>
>> Do you mean that you manually edited the prmtop file? This would
>> require
>> a great deal of study, enough probably to make you more of an expert on
>> this
>> subject than anyone on the mailing list.
>>
>> If you haven't done so, you should modify the parm.dat file (maybe that
>> is
>> what you meant?). Use parm91.dat as a template for the format of this
>> sort of
>> information. And, of course, test on a very small system, where you can
>> compute all of the terms by hand to compare.
>>
>> ...good luck...dac
>>
>>
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Received on Mon Feb 08 2010 - 13:00:02 PST
