You're trying to neutralize a positive charge with another positive
charge. Maybe try Cl?
For the non-integer charge, search the 'web' for the non-numerical part
of the error is a good strategy for life in general.
Look at the build-your-own residue tutorials to see how to solve the
missing type error.
Bill
On 5/11/19 4:16 AM, Sadaf Rani wrote:
> amber.ambermd.org
>
> Subject: The unperturbed charge of the unit: 4.003000 is not zero
> I am trying to generate parameters of my protein using following commands:-
>
> antechamber -i lig.pdb -fi pdb -o 1HVR_ligand.mol2 -fo mol2 -c bcc -pf yes
> -nc 0 -at gaff2 -j 5
> parmchk2 -i 1HVR_ligand.mol2 -f mol2 -o 1HVR_ligand.frcmod -s 2
>
> However I get following error message:-
>
> Added 21001 residues.
>> addIonsRand complex Na+ 0
> addIonsRand: 1st Ion & target are the same charge:
> can't neutralize.
>> saveamberparm complex complex.prmtop complex.inpcrd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: 4.003000 is not zero.
>
> FATAL: Atom .R<LIG 199>.A<C79 46> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C78 45> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C77 44> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C76 43> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C75 42> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C74 41> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C73 40> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C72 39> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C71 38> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C70 37> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C67 36> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C66 35> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C65 34> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C64 33> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C63 32> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C62 31> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C61 30> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C37 29> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C36 28> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C35 27> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C34 26> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C33 25> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C32 24> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C31 23> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C29 22> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C28 21> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C27 20> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C26 19> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C25 18> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C24 17> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C23 16> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C22 15> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C21 14> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C20 13> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C7 12> does not have a type.
> FATAL: Atom .R<LIG 199>.A<N7 11> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C6 10> does not have a type.
> FATAL: Atom .R<LIG 199>.A<O5 9> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C5 8> does not have a type.
> FATAL: Atom .R<LIG 199>.A<O4 7> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C4 6> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C3 5> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C2 4> does not have a type.
> FATAL: Atom .R<LIG 199>.A<N2 3> does not have a type.
> FATAL: Atom .R<LIG 199>.A<O1 2> does not have a type.
> FATAL: Atom .R<LIG 199>.A<C1 1> does not have a type.
> FATAL: Atom .R<HIE 168>.A<HD1 18> does not have a type.
> FATAL: Atom .R<CSO 166>.A<HD 9> does not have a type.
> FATAL: Atom .R<CSO 166>.A<H 8> does not have a type.
> FATAL: Atom .R<CSO 166>.A<OD 7> does not have a type.
> FATAL: Atom .R<CSO 166>.A<O 6> does not have a type.
> FATAL: Atom .R<CSO 166>.A<C 5> does not have a type.
> FATAL: Atom .R<CSO 166>.A<SG 4> does not have a type.
> FATAL: Atom .R<CSO 166>.A<CB 3> does not have a type.
> FATAL: Atom .R<CSO 166>.A<CA 2> does not have a type.
> FATAL: Atom .R<CSO 166>.A<N 1> does not have a type.
> FATAL: Atom .R<HIE 69>.A<HD1 18> does not have a type.
> FATAL: Atom .R<CSO 67>.A<HD 9> does not have a type.
> FATAL: Atom .R<CSO 67>.A<H 8> does not have a type.
> FATAL: Atom .R<CSO 67>.A<OD 7> does not have a type.
> FATAL: Atom .R<CSO 67>.A<O 6> does not have a type.
> FATAL: Atom .R<CSO 67>.A<C 5> does not have a type.
> FATAL: Atom .R<CSO 67>.A<SG 4> does not have a type.
> FATAL: Atom .R<CSO 67>.A<CB 3> does not have a type.
> FATAL: Atom .R<CSO 67>.A<CA 2> does not have a type.
> FATAL: Atom .R<CSO 67>.A<N 1> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> Can any one please suggest me.
>
> Thank you
>
> Sadaf
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Received on Sat May 11 2019 - 13:00:02 PDT
