AMBER Archive (2006)

Subject: Re: AMBER: Antechamber - NH2 and C not planar when it should be on one of my ligand

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Sat Jun 17 2006 - 03:28:55 CDT

Dear Chris,

In order to make it planar, the types of N3-N1-C7-N2, C7-H2-N2-H3 need to
have nonzero improper torsional parameters. I am not sure if antechamber
assigned the right atom types. As by looking at this structure, I would
guess that the type of N2 needs to be 'N2', but it is assigned as 'nh'
type. Good luck,

Best,

On Fri, 16 Jun 2006, Christophe Guilbert wrote:

> Hi everyone,
>
> I am using Antechamber 1.25 and Amber 8 (tleap ) to calculate the
> charges , topology and parameter of a ligand (see attachment in mol2)
> When I use CHARMM (using charmmgen) or my own program to minimized this
> ligand, I have C7 , N3, N1 and N2 becoming not planar after
> minimization. this structure contains 10 improper Angle (according to
> antechamber) , everything should be planar , I can only obtain a flat
> ligand when increasing the improper angle force constant from 1.1
> Kcal/mole to 10Kcal/mol. I don't see what's wrong with the topology and
> parameter. I would greatly appreciate any thought about it.
>
> Could anyone try my ligand and minimize it with Amber to check if they
> have the same result ?
>
> Here is my script
>
> antechamber -nc 1 -rn lig -i tobeconvert.mol2 -fi mol2 -o lig_bcc.mol2
> -fo mol2 -c bcc -j 4 -at gaff
> parmchk -i lig_bcc.mol2 -f mol2 -o lig_bcc.frcmod
>
> here is the leap.inp file:
> --------------------------------------------------
> source leaprc.gaff
> mods = LoadAmberParams lig_bcc.frcmod
> lig = loadMol2 lig_bcc.mol2
> saveAmberParm lig lig_bcc.prmtop lig_bcc.prmcrd
> quit
> ---------------------------------------------------
>
> tleap -f leap.inp
>
> Thanks
>
> Chris
>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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