Hi Cat,
The short answer is yes -- the protein parameters will still be ff99SB
if you use parmbsc0 parameters. My one suggestion would be to start
leap with leaprc.ff99bsc0 right from the beginning (as opposed to
leaprc.ff99SB), as this leaprc file automatically loads both the
ff99SB and parmbsc0 parameters.
Best,
Paul
On Aug 14, 2010, at 8:52 PM, Catein Catherine wrote:
>
> Dear Sir/Madam,
>
>
>
> I would like to include parmbsc0 for a protien DNA complex
> calculation.
>
>
>
> I tried to startup xleap using the following command:
>
>
>
> $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
>
>> source leaprc.gaff
>
>
>
> What can I do to include parmbsc0 force field for DNA parameters?
>
>
>
> If I call up the parmbsc0 force field parameters, will the
> parameters used for protein be still same as ff99SB?
>
>
>
> Best regards,
>
>
>
> Cat.
>
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Received on Sun Aug 15 2010 - 00:00:03 PDT
