On Tue, Feb 11, 2014, Jheng Wei Li wrote:
> I want to using PDB to create prmtop and inpcrd
> However, in my case, the molecule is protonated ammonia dimer, N2H7+.
> How do I set the residue name and force field to generate those 2 fiels?
>
> **********PDB**********
> ATOM 1 N1 ??? 1 0.000 0.000 -1.332 1.00 0.00
> ATOM 2 N2 ??? 1 0.000 0.000 1.339 1.00 0.00
> ATOM 3 H1 ??? 1 0.000 0.000 -0.128 1.00 0.00
> ATOM 4 H2 ??? 1 0.000 0.962 -1.702 1.00 0.00
> ATOM 5 H3 ??? 1 0.833 -0.481 -1.702 1.00 0.00
> ATOM 6 H4 ??? 1 -0.833 -0.481 -1.702 1.00 0.00
> ATOM 7 H5 ??? 1 -0.825 0.476 1.729 1.00 0.00
> ATOM 8 H6 ??? 1 0.825 0.476 1.729 1.00 0.00
> ATOM 9 H7 ??? 1 0.000 -0.952 1.729 1.00 0.00
> TER
> END
> **********PDB**********
Use a text editor to change the "???" to whatever 3-letter name you choose.
Generating the force field parameters will be a bigger challenge, since this
is a very unusual molecule. Check out the R.E.D. tools (RESP ESP Charge
Derive), or Wolf2Pack.
...dac
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Received on Tue Feb 11 2014 - 04:00:03 PST
