Thank you David,
I removed the minus signs and it made the NAN's go away.
I had been using CHARMM were the epsilons must be preceded by a minus.
Maybe that was the source of my error.
I obtained the parameters from published data and the charmm forcefield.
Regards
Greg
David A. Case wrote:
>On Fri, Jul 27, 2007, Greg Gannon wrote:
>
>
>
>>I am a new user of Amber. I wish to generate a prmtop file of a self
>>assembled monolayer.
>>Unfortunately my prmtop file (GTS.top) contains NAN in the FLAG
>>LENNARD_JONES_ACOEF section of the generated file.
>>
>>
>
>
>
>>NONB
>> AU 1.0370 -0.0780
>> S 2.1000 0.4700
>> HA 1.3200 -0.0220
>> H2 1.3400 0.0320
>> H3 1.3200 -0.0230
>> C2 2.0100 -0.0600
>> C3 2.0200 0.0730
>> A1 1.0370 -0.0780
>>
>>
>
>I'm pretty sure you can't have negative numbers in the "epsilon" column above.
>How did you generate these?
>
>...dac
>
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Received on Sun Jul 29 2007 - 06:07:38 PDT
