Dear All
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. Please let me know.
With my best regards
Sindrila
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Received on Sat Jan 14 2012 - 01:00:03 PST
