Hi,
I created some new lib, loaded them before loading the molecule, but I still
got FATAL errors of unrecognized atome types.
Could anyone please help to take a look at my steps below if I missed
something? Thanks in advance.
*> loadoff hiz.lib
Loading library: ./hiz.lib
Loading: hiz
> loadoff cym.lib
Loading library: ./cym.lib
Loading: cym
> loadoff hio.lib
Loading library: ./hio.lib
Loading: hio
> loadoff hia.lib
Loading library: ./hia.lib
Loading: hia
> ndm=loadpdb ndm-Zn.pdb
Loading PDB file: ./ndm-Zn.pdb
....
>solvateoct TIP3PBOX 12
>addions ndm Na+ 7
Done adding ions.
> saveamberparm ndm ../results/ndm.prmtop ../results/ndm.inpcrd
Checking Unit.
WARNING: There is a bond of 3.592209 angstroms between:
------- .R<HIZ 56>.A<ZN 18> and .R<HIE 58>.A<ND1 9>
WARNING: There is a bond of 4.573484 angstroms between:
------- .R<HIZ 56>.A<ZN 18> and .R<HIO 125>.A<NE2 11>
WARNING: There is a bond of 5.588924 angstroms between:
------- .R<ASP 60>.A<OD2 10> and .R<CYM 144>.A<ZN 11>
WARNING: There is a bond of 3.528961 angstroms between:
------- .R<HIA 95>.A<ZN 18> and .R<HIA 95>.A<OIA 24>
FATAL: Atom .R<HIZ 56>.A<N 1> does not have a type.
FATAL: Atom .R<HIZ 56>.A<H 2> does not have a type.
FATAL: Atom .R<HIZ 56>.A<CA 3> does not have a type.
FATAL: Atom .R<HIZ 56>.A<HA 4> does not have a type.
FATAL: Atom .R<HIZ 56>.A<ND1 5> does not have a type.
FATAL: Atom .R<HIZ 56>.A<HD1 6> does not have a type.
FATAL: Atom .R<HIZ 56>.A<CG 7> does not have a type.
FATAL: Atom .R<HIZ 56>.A<CB 8> does not have a type.
FATAL: Atom .R<HIZ 56>.A<HB3 9> does not have a type.
FATAL: Atom .R<HIZ 56>.A<HB2 10> does not have a type.
FATAL: Atom .R<HIZ 56>.A<NE2 11> does not have a type.
FATAL: Atom .R<HIZ 56>.A<CD2 12> does not have a type.
FATAL: Atom .R<HIZ 56>.A<HD2 13> does not have a type.
FATAL: Atom .R<HIZ 56>.A<CE1 14> does not have a type.
FATAL: Atom .R<HIZ 56>.A<HE1 15> does not have a type.
FATAL: Atom .R<HIZ 56>.A<C 16> does not have a type.
FATAL: Atom .R<HIZ 56>.A<O 17> does not have a type.
FATAL: Atom .R<HIZ 56>.A<ZN 18> does not have a type.
FATAL: Atom .R<HIA 95>.A<N 1> does not have a type.
FATAL: Atom .R<HIA 95>.A<H 2> does not have a type.
FATAL: Atom .R<HIA 95>.A<CA 3> does not have a type.
FATAL: Atom .R<HIA 95>.A<HA 4> does not have a type.
FATAL: Atom .R<HIA 95>.A<ND1 5> does not have a type.
FATAL: Atom .R<HIA 95>.A<HD1 6> does not have a type.
FATAL: Atom .R<HIA 95>.A<CG 7> does not have a type.
FATAL: Atom .R<HIA 95>.A<CB 8> does not have a type.
FATAL: Atom .R<HIA 95>.A<HB3 9> does not have a type.
FATAL: Atom .R<HIA 95>.A<HB2 10> does not have a type.
FATAL: Atom .R<HIA 95>.A<NE2 11> does not have a type.
FATAL: Atom .R<HIA 95>.A<CD2 12> does not have a type.
FATAL: Atom .R<HIA 95>.A<HD2 13> does not have a type.
FATAL: Atom .R<HIA 95>.A<CE1 14> does not have a type.
FATAL: Atom .R<HIA 95>.A<HE1 15> does not have a type.
FATAL: Atom .R<HIA 95>.A<C 16> does not have a type.
FATAL: Atom .R<HIA 95>.A<O 17> does not have a type.
FATAL: Atom .R<HIA 95>.A<ZN 18> does not have a type.
FATAL: Atom .R<HIA 95>.A<CI 19> does not have a type.
FATAL: Atom .R<HIA 95>.A<OI 20> does not have a type.
FATAL: Atom .R<HIA 95>.A<OXI 21> does not have a type.
FATAL: Atom .R<HIA 95>.A<CHI 22> does not have a type.
FATAL: Atom .R<HIA 95>.A<CIA 23> does not have a type.
FATAL: Atom .R<HIA 95>.A<OIA 24> does not have a type.
FATAL: Atom .R<HIA 95>.A<OXA 25> does not have a type.
FATAL: Atom .R<HIA 95>.A<CHA 26> does not have a type.
FATAL: Atom .R<HIO 125>.A<N 1> does not have a type.
FATAL: Atom .R<HIO 125>.A<H 2> does not have a type.
FATAL: Atom .R<HIO 125>.A<CA 3> does not have a type.
FATAL: Atom .R<HIO 125>.A<HA 4> does not have a type.
FATAL: Atom .R<HIO 125>.A<ND1 5> does not have a type.
FATAL: Atom .R<HIO 125>.A<HD1 6> does not have a type.
FATAL: Atom .R<HIO 125>.A<CG 7> does not have a type.
FATAL: Atom .R<HIO 125>.A<CB 8> does not have a type.
FATAL: Atom .R<HIO 125>.A<HB3 9> does not have a type.
FATAL: Atom .R<HIO 125>.A<HB2 10> does not have a type.
FATAL: Atom .R<HIO 125>.A<NE2 11> does not have a type.
FATAL: Atom .R<HIO 125>.A<CD2 12> does not have a type.
FATAL: Atom .R<HIO 125>.A<HD2 13> does not have a type.
FATAL: Atom .R<HIO 125>.A<CE1 14> does not have a type.
FATAL: Atom .R<HIO 125>.A<HE1 15> does not have a type.
FATAL: Atom .R<HIO 125>.A<C 16> does not have a type.
FATAL: Atom .R<HIO 125>.A<O 17> does not have a type.
FATAL: Atom .R<HIO 125>.A<OZ 18> does not have a type.
FATAL: Atom .R<CYM 144>.A<ZN 11> does not have a type.
Failed to generate parameters
Parameter file was not saved.*
Please help. Thank you.
Chinsu
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Received on Mon May 09 2011 - 01:30:02 PDT
