[AMBER] Info: Bond types are assigned for valence state 5 with penalty of 1

From: Atila Petrosian <atila.petrosian.gmail.com>
Date: Tue, 6 Oct 2015 00:27:53 +0330

Dear amber users

I want to obtain prmtop and inpcrd files for my ligand.

Please find the lig.pdb file in the followimg link:

https://www.dropbox.com/s/4kvb8zt6mkd8fq0/lig.pdb?dl=0
https://www.dropbox.com/s/fg2xzxsl0cnd1cx/lig.png?dl=0

Based on experimental data, It should be special charges on the some atoms.
For example:

13(O1A)=-1
18(O2B)=-1
19(N3)=+1

Should I use -nc in antechamber?

I want to have resp charges for my ligand. For this aim,
I used (HF/6-31G(d,p) SCF=Tight Pop=MK IOp(6/33=2)) in gaussian.

Please find the lig.gjf and g09.out files, in the followimg links,
respectively:

https://www.dropbox.com/s/ww18dk5o4gsucfu/lig.com?dl=0
https://www.dropbox.com/s/d947ekkfpbny72h/g09.out?dl=0

When I use antechamber,

$AMBERHOME/exe/antechamber -i g09.out -fi gout -o lig.mol2 -fo mol2 -c resp

lig.mol2 file was created. But, I encountered with

Info: Bond types are assigned for valence state 5 with penalty of 1

Is it true? Can I continue?

Please guide me.
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Received on Mon Oct 05 2015 - 14:00:03 PDT