Hi, thanks for reporting this issue. We usually assign the default value of
"1.1 180.0 2.0" for improper parameters. Unfortunately, for your molecule
ITD, the force constant is too small. Please use a larger value for the
following parameter:
na-nc-cd-ss 10.5 180 2.0
You should be able to solve this problem.
All the best,
Junmei
On Tue, Mar 4, 2025 at 5:17 AM YOKOI Taiyo via AMBER <amber.ambermd.org>
wrote:
> Hi,
>
> I encountered a problem when parametrizing a ligand containing a 5,5-fused
> aromatic system, specifically imidazo[2,1-b][1,3,4]thiadiazole.
> Using the input structure obtained from PubChem (
> https://pubchem.ncbi.nlm.nih.gov/compound/88013-15-4), I executed the
> following commands.
>
> ```
> antechamber -i ITD.sdf -fi sdf -o ITD_abcg2.mol2 -fo mol2 -c abcg2 -at
> gaff2 -nc 0 -rn LIG
> parmchk2 -i ITD_abcg2.mol2 -o ITD_abcg2.frcmod -f mol2 -s gaff2
> ```
>
> Then I executed tleap to obtain the prmtop and inpcrd files.
>
> ```
> source leaprc.gaff2
> source leaprc.water.tip3p
> lig = loadMol2 ITD_abcg2.mol2
> loadAmberParams ITD_abcg2.frcmod
> solvateBox lig TIP3PBOX 10.0
> saveAmberParams lig lig.prmtop lig.inpcrd
> quit
> ```
>
> After energy minimization, I got a strange structure in which the fused
> system bended at the bridgehead position (see minimized.png).
> At first, I thought this was caused by IMPROPER parameters written in the
> frcmod file. But the parameters seem OK as the default values for the
> benzene ring was assigned for the bridge head positions (see lig.frcmod and
> atomtype.png).
> How can I solve this issue? I would appreciate your help.
>
> Best regards,
>
> Taiyo Yokoi _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Mar 10 2025 - 08:30:02 PDT
