On Sun, Sep 04, 2011, tsurma.umich.edu wrote:
>
> In leap, I have a system of 290 TP4 water molecules. Now, how do I replace
> one H2O molecule (unit) by one CYN unit (for which I have loaded prepc and
> frcmod file). Or, two TP4 molecules by two CYN units?
>
> I looked up in Ambertools manual but couldn't get the add command to work,
> I am doing some basic mistake!!
I don't think there is a command to do what you want. It would not be "add",
whose description says "This command is used to place ATOMs within RESIDUEs,
and RESIDUEs within UNITs." That is not what you want to do.
I think you have start fresh. You could manually edit the pdb file that has
just waters in it, replacing some of the waters with CYN. Then usd loadPdb
to create a new unit from that PDB file.
....dac
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Received on Mon Sep 05 2011 - 17:30:02 PDT
