Hi Aishwarya:
The libraries are in $AMBERHOME/dat/leap/lib/oldff, the same will happen
with the prep files.
The solution to your problem is to include the path of all the other oldff
directories in your leap or tleap command using the -I option.
leap -I $AMBERHOME/dat/leap/cmd/oldff -I $AMBERHOME/dat/leap/lib/oldff -I
....
You will need to add another directory.
After including the directories use leap as usual:
source leaprc.ff02pol.r1
because now all the directories are in the leap searching path.
Hope this helps!
Regards,
Anthony Cruz
Graduate student
CUNY Graduate Center
Lehman College
Kurtzman Lab
On Mon, Aug 7, 2017 at 2:41 PM, Aishwarya Venkatramani <avenkatr.ucsd.edu>
wrote:
> 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Aishwarya
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Aug 07 2017 - 13:00:02 PDT
