Hi Albert,
You don't state how your prepared g2a.pdb. It looks like your atom naming
is incorrect. Firstly I believe the residue name should be PPC for the
entire lipid. If you run leap and load PPC.lib and then edit PPC you can
choose to turn on the atom names in the menu and you'll be able to see
what atom names leap expects.
All the best
Ross
On 11/13/12 2:18 AM, "Albert" <mailmd2011.gmail.com> wrote:
>hello:
>
> I am using the following command to generate a membrane system for
>POPC GAFF:
>
>tleap -s -f leaprc.ff12SB
>
>source leaprc.gaff
>source GAFFlipid.dat
>loadamberparams GAFFlipid.frcmod
>loadoff PPC.lib
>loadamberparams ligand.frcmod
>loadoff ligand.lib
>
>mol = loadpdb g2a.pdb
>saveamberparm mol sys.prmtop sys.inpcrd
>
>
>but it said:
>
>FATAL: Atom .R<OL 997>.A<C18 19> does not have a type.
>FATAL: Atom .R<OL 997>.A<H8R 20> does not have a type.
>FATAL: Atom .R<OL 997>.A<H8S 21> does not have a type.
>FATAL: Atom .R<OL 997>.A<C19 22> does not have a type.
>FATAL: Atom .R<OL 997>.A<H9R 23> does not have a type.
>FATAL: Atom .R<OL 997>.A<C110 24> does not have a type.
>FATAL: Atom .R<OL 997>.A<H10R 25> does not have a type.
>FATAL: Atom .R<OL 997>.A<C111 26> does not have a type.
>FATAL: Atom .R<OL 997>.A<H11R 27> does not have a type.
>FATAL: Atom .R<OL 997>.A<H11S 28> does not have a type.
>FATAL: Atom .R<OL 997>.A<C112 29> does not have a type.
>FATAL: Atom .R<OL 997>.A<H12R 30> does not have a type.
>FATAL: Atom .R<OL 997>.A<H12S 31> does not have a type.
>FATAL: Atom .R<OL 997>.A<C113 32> does not have a type.
>FATAL: Atom .R<OL 997>.A<H13R 33> does not have a type.
>FATAL: Atom .R<OL 997>.A<H13S 34> does not have a type.
>FATAL: Atom .R<OL 997>.A<C114 35> does not have a type.
>FATAL: Atom .R<OL 997>.A<H14R 36> does not have a type.
>FATAL: Atom .R<OL 997>.A<H14S 37> does not have a type.
>FATAL: Atom .R<OL 997>.A<C115 38> does not have a type.
>FATAL: Atom .R<OL 997>.A<H15R 39> does not have a type.
>FATAL: Atom .R<OL 997>.A<H15S 40> does not have a type.
>FATAL: Atom .R<OL 997>.A<C116 41> does not have a type.
>FATAL: Atom .R<OL 997>.A<H16R 42> does not have a type.
>FATAL: Atom .R<OL 997>.A<H16S 43> does not have a type.
>FATAL: Atom .R<OL 997>.A<C117 44> does not have a type.
>FATAL: Atom .R<OL 997>.A<H17R 45> does not have a type.
>FATAL: Atom .R<OL 997>.A<H17S 46> does not have a type.
>FATAL: Atom .R<OL 997>.A<C118 47> does not have a type.
>FATAL: Atom .R<OL 997>.A<H18R 48> does not have a type.
>FATAL: Atom .R<OL 997>.A<H18S 49> does not have a type.
>FATAL: Atom .R<OL 997>.A<H18T 50> does not have a type.
>
>
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Received on Tue Nov 13 2012 - 09:30:03 PST
