Hi Case,
Thank you so much!
~Surma
On Mon, 5 Sep 2011 20:11:46 -0400, case <case.biomaps.rutgers.edu> wrote:
> 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 Tue Sep 06 2011 - 09:00:02 PDT
