On Fri, May 20, 2005, chaiann ng wrote:
>
> I am trying to read the pdb back to leap and output prmtop and inpcrd after
> the dynamic of solvation of chloroform box.
>
> I read in leaprc.gaff; leaprc.ff03; loadOff by lib, load frcmod.chcl3, when
^^^^^^^^^^^^^^
I' not sure what you mean by the above...
> i loadpdb in and try to output inpcrd and prmtop, this is what i get.
>
> Creating new UNIT for residue: CL3 sequence: 403
> Created a new atom named: H1 within residue: .R<CL3 403>
> Created a new atom named: C1 within residue: .R<CL3 403>
> Created a new atom named: CL1 within residue: .R<CL3 403>
> Created a new atom named: CL2 within residue: .R<CL3 403>
> Created a new atom named: CL3 within residue: .R<CL3 403>
>
> If I also load chcl3.in then i get this.
You definitely have to do this, so that leap knows about the CL3 unit.
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-H1-C1-*
> +--- With Sp0 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
Check your output to make sure leap is not trying to add some x-H1-C1-x
torsion; be sure to put TER cards in your pdb file between each separate
molecule. It could be that leap is trying to make a covalent link between the
chloroform and some previous residue.
Why are you trying to do this, anyway?
....dac
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Received on Fri May 20 2005 - 02:53:04 PDT
