Dear Chris,
In theory you can do it because you can get the topologies for your
small molecules with antechamber and on the other hand, you have the
force field, for example leaprc.gaff for your small molecule, so it
would be the same that for the case in which your system is a protein
with its respective force field (leaprc.ff99SB).
Good luck
On Mon, 4 Jun 2012 21:37:51 -0700 (PDT), Chris Chris
<alpharecept.yahoo.com> wrote:
> I have a pdb file comprised of Methylsalicylate and
> Polyethyleneglycol (PEG) 4000. Can I perform molecular dynamics on
> this system as there is no protein component? I know I can use
> Antechamber to devlop the prmtop files for each molecule separately,
> however- the "complex" will not have a protein component and I'm not
> sure this will work.
>
> If anyone has a suggestion to how to model this problem on another
> platform, I'd be also grateful.
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Received on Mon Jun 04 2012 - 22:30:03 PDT
