On Wed, Mar 23, 2016, A kS wrote:
>
> I was have an idea that if the PDB does not have residue name S2P LEaP will
> not include the parameter of frcmod_s2p.
This is not correct, as Dan pointed out earlier. However, if the PDB file
does not have an S2P residue, why do you wish to load the frcmod_s2p file?
>
> Now I am totally confused, it seems that I can not include frcmod of bsc0
> with protein force field to simulate a protein DNA complex because DNA may
> have some bonds that are common with protein and then those bond of
> protein will also get modify.
This is not generally a problem: look at what is done in leaprc.ff14SB, which
loads both protein and nucleic acid parameters. You may need to be careful
if you have both phosphorylated amino acids and nucleic acids in the same
system -- I don't know if there is overlap of parameters there or not.
>
> I am really clueless please help.
Saying that you are "afraid" or "clueless" is not of much help. Try to
formulate as specific a question as you can.
...dac
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Received on Thu Mar 31 2016 - 05:00:03 PDT
