Hi Albert,
It looks like your POPC bilayer is in lipid11 pdb format.
Cheers,
Callum
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of Albert [mailmd2011.gmail.com]
Sent: 13 November 2012 10:18
To: AMBER Mailing List
Subject: [AMBER] problem for lipid GAFF
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 - 09:30:02 PST
