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Hi everyone I'm looking for parameters for an MD simulation for 2-Aminoisobutyric acid. Anyone knows if their are available parameters for this molecule? I searched the forum here and also tried using CCGenFF and SwissParam but the results were not sufficient.

Thanks in advance to all repliers!

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There is nothing strange with this residue, so paramchem should be able to deal with it rather easily. What does "not sufficient" mean?


Lennart Nilsson
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My intention in "not sufficient" is that it rated very high penalty scores for the ATOM N and CA as well as for the CG301 NG3P3 HGP2 angle which doesn't seem to make a lot of sense to me since their is nothing unusual about them to the best of my understanding. Here's the info from ParamChem:

* Toppar stream file generated by
* CHARMM General Force Field (CGenFF) program version 1.0.0
* For use with CGenFF version 3.0.1
*

read rtf card append
* Topologies generated by
* CHARMM General Force Field (CGenFF) program version 1.0.0
*
36 1

! "penalty" is the highest penalty score of the associated parameters.
! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

RESI Molecu 0.000 ! param penalty= 20.500 ; charge penalty= 177.504
GROUP ! CHARGE CH_PENALTY
ATOM N NG3P3 -0.346 ! 176.787
ATOM HT1 HGP2 0.330 ! 4.450
ATOM HT2 HGP2 0.330 ! 4.450
ATOM HT3 HGP2 0.330 ! 4.450
ATOM CA CG301 0.255 ! 177.504
ATOM C CG2O3 0.301 ! 23.734
ATOM OCT1 OG2D2 -0.600 ! 1.950
ATOM OCT2 OG2D2 -0.600 ! 1.950
ATOM CB1 CG331 -0.270 ! 13.500
ATOM CB2 CG331 -0.270 ! 13.500
ATOM HB11 HGA3 0.090 ! 1.950
ATOM HB12 HGA3 0.090 ! 1.950
ATOM HB13 HGA3 0.090 ! 1.950
ATOM HB21 HGA3 0.090 ! 1.950
ATOM HB22 HGA3 0.090 ! 1.950
ATOM HB23 HGA3 0.090 ! 1.950

BOND N CA
BOND CA C
BOND C OCT1
BOND CA CB1
BOND CA CB2
BOND CB1 HB11
BOND CB1 HB12
BOND CB1 HB13
BOND N HT1
BOND N HT2
BOND N HT3
BOND C OCT2
BOND CB2 HB21
BOND CB2 HB22
BOND CB2 HB23
IMPR C OCT2 OCT1 CA

END

read param card flex append
* Parameters generated by analogy by
* CHARMM General Force Field (CGenFF) program version 1.0.0
*

! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

BONDS
CG301 NG3P3 200.00 1.4800 ! Molecu , from CG314 NG3P3, penalty= 9

ANGLES
CG2O3 CG301 NG3P3 43.70 110.00 ! Molecu , from CG2O3 CG314 NG3P3, penalty= 9
CG331 CG301 NG3P3 67.70 110.00 ! Molecu , from CG331 CG314 NG3P3, penalty= 9
CG301 NG3P3 HGP2 30.00 109.50 20.00 2.07400 ! Molecu , from CG324 NG3P3 HGP2, penalty= 20.5

DIHEDRALS
OG2D2 CG2O3 CG301 NG3P3 3.2000 2 180.00 ! Molecu , from OG2D2 CG2O3 CG314 NG3P3, penalty= 9
NG3P3 CG301 CG331 HGA3 0.2000 3 0.00 ! Molecu , from NG3P3 CG314 CG331 HGA3, penalty= 9
CG2O3 CG301 NG3P3 HGP2 0.1000 3 0.00 ! Molecu , from CG2O3 CG314 NG3P3 HGP2, penalty= 9
CG331 CG301 NG3P3 HGP2 0.1000 3 0.00 ! Molecu , from CG331 CG314 NG3P3 HGP2, penalty= 9

IMPROPERS

END
RETURN

Last edited by Yoav Raz; 06/04/15 12:01 PM.
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I think you should be able to just replace HA with a methyl (the same as the Ala side chain), and adjust the CA charge and atom type.


Lennart Nilsson
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If you submitted the zwitterion single amino acid to ParamChem, the result will be dominated by end effects from the charged groups.

If this is intended for use within a peptide chain, I suggest using a neutral molecule with peptide capping groups, such as acetyl for the amino group and methylamine for the carboxyl, e.g.

CH3-CO-NH-C(CH3)2-CO-N-CH3

I'd probably also submit the two cases with only one end capped.


Rick Venable
computational chemist

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thank you very much for your help, much appreciated!

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Hi Yoav, sorry for my late reply. We've actually done a full parametrization of the non-coded amino acid AIB in a peptide/protein context, including CMAP. I won't post it here because the experimental validation and fine-tuning is still in progress (it got put on the backburner in favor of other projects), but if you send me a personal e-mail explaining what you want to use it for, I may share it with you.

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Great Kenno, I pmed you regarding this matter.

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Kenno,
Our team is testing the effects of the dehydroamino acids on peptide structure. We finished the parameterization of our dehydroresidue but have been unable to understand the correct way to append our new residue to the existing CMAP. We have read over the files parmfile.doc and io.doc as a team and are still unsure how to add to CMAP. What would you recommend us do next since you successful did it for the amino acid AIB. Thank you!

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See also rtop.doc, which documents the CMAP statement used in RESIdue definitions.


Rick Venable
computational chemist


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