When I run the script again with the change oldff/leaprc.ff02pol.r1
ff02 is loaded correctly, but I get this error:
Could not open file all_nucleic02.lib: not found
Could not open database: all_nucleic02.lib
Could not open file all_amino02.r1.lib: not found
Could not open database: all_amino02.r1.lib
Could not open file all_aminoct02.lib: not found
Could not open database: all_aminoct02.lib
Could not open file all_aminont02.lib: not found
Could not open database: all_aminont02.lib
When I look at $AMBERHOME/dat/leap/lib these library files are
not present. Will I have to load them from somewhere else?
Thanks,
Aishwarya
On Fri, Aug 4, 2017 at 11:18 AM, David A Case <dacase.chem.rutgers.edu>
wrote:
> On Fri, Aug 04, 2017, Aishwarya Venkatramani wrote:
>
> > Could not open file leaprc.ff02: not found
>
> You have to read the manual carefully (and maybe we should try to make this
> more prominent.) ff02 and related force fields are listed in Section
> 3.9 as "obsolete force fields". At the beginning of that section, it says
> "The leaprc files that load these files have been moved to
> $AMBERHOME/dat/leap/parm/oldff" -- that is actually a typo: should be
> $AMBERHOME/dat/leap/cmd/oldff. (I'll submit a fix to the manual.)
>
> So: you need to tell tleap to "source oldff/leaprc.ff02pol.r1" -- you
> almost
> certainly want the "revised" parameters, as described in section 3.9.4
> of the Reference Manual.
>
> If you are serious about such simulations, you might want to contact Prof.
> Yong Duan at UC Davis, to see if he has more recent parameters that he
> might
> want to recommend.
>
> ....dac
>
>
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>
--
Aishwarya
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Received on Mon Aug 07 2017 - 12:00:02 PDT
