Dear David
Thank you for your reply and suggestion.. Actually tried to setup my system
first without loading inos94.lib but i received an error regarding Mg+2
ions, so just to remove that error I Ioaded ions94.lib.
Best
Sumra Wajid Abbasi
PhD Scholar
Computational Biology Lab, National Center for Bioinformatics
Quaid-e-Azam University, Islamabad-45320 Pakistan.
On Thu, Nov 12, 2015 at 5:42 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Thu, Nov 12, 2015, Sumra Wajid Abbasi 30-FBAS/MSBI/F09 wrote:
>
> > *> loadoff ions94.lib*
>
> Ooooh...this is way way old. The "modern" leaprc files in Amber load
> atomic_ions.lib. Depending on what leaprc file you used for your protein
> (leaprc.ff14SB is generally the best choice, but see the manual for more
> details), atomic_ions.lib would have been already loaded. By loading
> ions94.lib afterwards, you are replacing the current/correct ion
> descriptions
> with ones that are more than 20 years old.
>
> Bottom line: don't load ions94.lib.
>
> [Developers: we "hide" old leaprc files in an oldff subdirectory, but
> don't do
> the same for library or parameter files. There would be some work
> involved in
> doing this, but it would probably help users avoid problems like this.]
>
> ....dac
>
>
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Received on Fri Nov 13 2015 - 23:30:03 PST
