On Sat, Jan 14, 2012, Sindrila Dutta banik wrote:
>
> I want to know a very simple question regarding the 'tleap'. When
> I load a library file using "$AMBERHOME/exe/xleap -s -f
> $AMBERHOME/dat/leap/cmd/leaprc.ff99SB" command and use "list" command
> to show the defined residues it shows a long list (more than 100) of
> templates. It contains residue template for different amino acids,
> nucleic acids as well as water such as TP3, TP4, TIP3PBOX, TIP4PBOX etc.
>
> Now if I change the force filed from leaprc.ff99SB to leaprc.ff94 or
> leaprc.ff96 the parameters for the amino acid system and nucleic acid
> system (such as ALA, DT, TYR, PRO etc) will change but not for the water
> such as TP3, TP4, TIP3PBOX, TIP4PBOX. The defined residues such as 'TP3,
> TP4, TIP3PBOX, TIP4PBOX' independent of force field loaded in the first
> step. Now I want to be sure.
The leaprc files are simple text files of commands that LEaP will run.
You can look at the files, and see exactly which libraries are being loaded.
You will see that (for your example) both files load the same "solvents.lib"
file, so water models and other solvents will be unchanged.
Please note that we strongly discourage people from using the very old
ff94 and ff96 force fields.
...dac
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Received on Sat Jan 14 2012 - 06:30:03 PST
