On Thu, Mar 07, 2019, Vikram Dalal wrote:
>
>I have to do protein DNA molecular dynamics in AMBER.
>
>I am able to generate the paramtop and inpcrd for DNA and protein by using
>OL15 force field and ffs14SB, respectively.
>
>I do not know how to merge these both files for further molecular dynamics.
You don't merge the two prmtop/inpcrd files.
Rather, in tleap you would source both leaprc.protein.ff14SB and
leaprc.DNA.OL15 (see note 2 on p. 33 of the Amber 2018 Reference
Manual). Then, you would use the loadPdb command to load a pdb file
that had both the protein and the DNA in the same file (separated by a
TER card). Then continue.
....hope this helps....dac
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Received on Thu Mar 07 2019 - 06:30:03 PST
