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NMA parameters
#7989 08/23/05 11:39 PM
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Dear CHARMMers,

I have a question to parametrize N-methylacetamide (NMA).
In the CHARMM topology file (top_all22_model.inp), the structure of NMA is designed to optimize the trans-NMA (cis-cis) structure according to the terminology of Nandini and Sathyanarayana (J. Mol. Struct. Theochem 579 (2002) 1-9). According to their study, there are several stable structures for NMA even in vacuum. I am wondering whether it is acceptable to change the dihedral angle in the IC table to have different NMA conformers or not.

I appreciate your comments.

Best wishes,

Re: NMA parameters
fujisaki #7990 08/24/05 12:12 AM
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Not a problem-- but the IC table is used mostly for coordinate building and analysis, and has no impact on energetics.


Rick Venable
computational chemist

Re: NMA parameters
rmv #7991 08/24/05 12:57 PM
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note that the peptide bond in NMA (and the peptide bond in general) was optimized to be planar in charmm. however, the peptide bond around the nitrogen is pyramidal in the gas phase. the reason the structure is planar in charmm is due to hydrogen bonding of the peptide bond leading to a change in hybridization, such that the planar structure is more stable.

alex


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Re: NMA parameters
alex #7992 08/24/05 06:58 PM
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Dear Rick and Alex,

Thanks for your replies and useful information.
I have a further problem now. I am trying to rotate
the methyl groups in NMA by modifying the topology file
(top_all22_model.inp), but it does not seems to work.
Which file and which parameters should I modify to rotate the methyl group, say, by 60 degrees around the CN or CC axis?

I appreciate your help.

Best wishes,

Re: NMA parameters
fujisaki #7993 08/24/05 07:44 PM
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That depends somewhat on how you are obtaining Cartesian coords, and what you're trying to do. Note that changing the IC data in the toplogy file has no effect unless you're using IC BUILD to create Cartesian coords.

Assuming you have coords, one way is to define an axis along the bond with COOR AXIS (and a double atom selection), and then use COOR ROTA AXIS to rotate the methyl group (via an atom selection) around that axis.

corman.doc
select.doc


Rick Venable
computational chemist

Re: NMA parameters
rmv #7994 08/25/05 12:34 PM
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it is not clear what you are trying to do. do you want the minimized structure to have the methyl hydrogens rotated by 60 deg.?

alex


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201
Re: NMA parameters
alex #7995 08/25/05 03:42 PM
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Dear Rick and Alex,

What I want to do is to have a stable structure of NMA with (one of or both of) methyl group rotated by 60 degees. So I need to modify the parameter file, but I can't understand which parameters I have to choose. I thought I need to modify the following dihedral angles

HA CT3 NH1 C
O C CT3 HA

but the parameter file assumes that their potential barriers are zero! So I am wondering why NMA become a stable structure ...

I appreciate your comments.

Best wishes,

Re: NMA parameters
fujisaki #7996 08/25/05 06:16 PM
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Rotation of methyl groups hasn't been a dominant focus of CHARMM parameter development; it's not as easy as it might seem, as there are quantum effects involved in that fairly rapid rotation. For NMA itself, the principal torsional term is likely that for CT3-C-NH1-CT3, and an improper torsion for the planar C=O group. The rotational barriers for the CH3 group are probably mostly based on VDW interactions; you should write a script to compute the energy as function of CH3 rotation.


Rick Venable
computational chemist

Re: NMA parameters
rmv #7997 08/26/05 02:25 PM
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Dear Rick,

Thanks for your help.

I calculated the potential energy as a function of the methyl group rotation angle (while other atoms fixed), and found that the structure I found is the only minimum. The barrier height is about 0.8 kcal/mol, and it comes from, as Rick said, the VDW interaction (attraction) because there is no dihedral interaction as I mentioned. On the other hand, Guo and Karplus (J.Phys.Chem.96(1992)7273) found that the barrier height is about 0.1 kcal/mol for NMA in vacuum by the ab initio method, so this means that the CHARMM potential is too high for the methyl group rotation. That is, CHARMM is not so reliable when we consider the methyl group rotation!

Re: NMA parameters
rmv #7998 08/27/05 02:26 PM
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electrostatics will also play a role, but that's besides the point. if the orienation of the methyl groups is that important, do QM surface of the rotation and then adjust the dihedral parameters for the terms you listed above to reproduce the QM surfaces. A single 3 fold term with a relatively small force constant should be adequate. switching the phase between 0 and 180 will allow you to control the orientation of the methyl hydrogens.

alex


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201
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