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Parameters for Ammonium ion
#29374 02/21/12 03:32 PM
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shrek Offline OP
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Dear Forum members,

I had a question regarding Ammonium ions. CHARMM-GUI has the parameters for Ammonia and for Tetramethyl and methyl ammonium ions. Naively speaking I ought to use the tetramethy ammonium for obtaining the dihedral and the angle information due to the symmetry of the problem.

Would that be an accurate assumption?

Also, could you please suggest any other pitfalls for using Tetramethyl ammonium ions?

The only discussion on the issue I could find on the website was:
http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27271

Thanks in advance!

Sincerely,
Shrek

Re: Parameters for Ammonium ion
shrek #29376 02/21/12 06:07 PM
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Do I understand correctly that you want to simulate [anorganic] ammonium ions in solution? If yes, which dihedrals are you talking about?

Re: Parameters for Ammonium ion
Kenno #29394 02/23/12 11:15 AM
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shrek Offline OP
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Sorry. There are no dihedrals to talk of. All I should ask is Angle information.

And yes, I wanted the inorganic Ammonium parameters.

Thanks!

Last edited by shrek; 02/23/12 11:15 AM.
Re: Parameters for Ammonium ion
shrek #29415 02/24/12 06:22 PM
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In your first post, you asked about the pitfalls of using tetramethylammonium as a starting point. These include:
  • the nitrogen L-J parameters being totally shielded from the solvent by the methyl groups,
  • methyl groups having totally different electrostatic/electronegativity properties than hydrogens,
  • methyl groups having totally different bonded properties than hydrogens.
In summary, of all the protonated amines, tetramethyl ammonium is the worst possible starting point for assigning ammonium parameters. Rather, the staring point of choice would be methylammonium (RESI MAMM). You can just keep the same atom types and have 0 missing parameters; I strongly feel the existing methylammonium parameters are very suitable for ammonium. As for the charges, you can just set all 4 hydrogens to 0.33 (the value in MAMM), and adjust the nitrogen by -0.02 so that the total charge is +1. Finished!

Re: Parameters for Ammonium ion
Kenno #29442 02/27/12 10:27 AM
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shrek Offline OP
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Thank you Kenno. This was really helpful and I feel was adequate for my needs! Great help. Cheers!

Last edited by shrek; 02/27/12 10:27 AM.
Re: Parameters for Ammonium ion
Kenno #37622 08/20/19 07:17 PM
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I was also trying to parameterize ammonium too and was wondering how we would adjust the IC commands from the MAMM file to correct for ammonium.

For MAMM it currently looks like this:

IC NZ HE3 *CE HE1 0.0000 0.00 120.00 0.00 0.0000
IC NZ HE3 *CE HE2 0.0000 0.00 -120.00 0.00 0.0000
IC HE3 CE NZ HZ3 0.0000 0.00 180.00 0.00 0.0000
IC CE HZ3 *NZ HZ1 0.0000 0.00 120.00 0.00 0.0000
IC CE HZ3 *NZ HZ2 0.0000 0.00 -120.00 0.00 0.0000


not sure how to adjust to account for the H.

Thank you !

Re: Parameters for Ammonium ion
shrek #37623 08/20/19 07:29 PM
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The IC table is not used for any energy calculations, so you don't need it; it can be used for model building, and in this case the 0.0 entries should be filled in using values in the parameter file (see intcor.doc/intcor.info).
Eg, if you have coordinates for part of the system:
IC FILL
IC PARA
IC BUILD

Hydrogens are a particular case, and are best placed (given coordinates) using the HBUIld command.

You should read the CHARMM papers (the JCC 2009 paper is a good starting point) and have a look at some of the basic examples in Script Archive Forum


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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