Hello David,
I use AMBER 9. I deleted the original force-field files in leap. And then copy the new forcefield files which i download from AMBER homepage.
Now i can loadoff ions08.lib, type 'list', i can see F- Br- I- etc.
I load the NaF.pdb, it was successful, no error. using NaF=loadpdb NaF.pdb
But i type 'saveAmberParm NaF NaF.top NaF.crd' there were error,
could not find type: Na+
could not find type: F-
How can i save this .pdb file to .top and .crd??
I saw the mannual : to use the newer versions, you will need to load the ions08.lib file as well as the appropriate frcmod file.
How can i achieve this aim?
Thanks
Tiefeng
At 2011-04-18 20:04:04，"David A Case" <case.biomaps.rutgers.edu> wrote:
>On Mon, Apr 18, 2011, MD wrote:
>
>> I'd like to add ions to water, using the following command,
>>
>> a= SPCBOX
>> I want the ions randomly packed in the water box, how can i achieve this purpose?
>
>The recommended approach is to choose a single water molecule as the "solute",
>then use solvateBox and addIons to prepare the simulation.
>
>....good luck...dac
>
>
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Received on Tue Apr 19 2011 - 00:30:04 PDT
