[gmx-users] Regarding the topology of triethylammonium ion generated using TPPMKTOP

[Justin Lemkul]

On 7/25/16 5:11 AM, soumadwip ghosh wrote:
> Hi,
>     I have recently used the TPPMKTOP topology builder for obtaining a
> topology for triethylammonium ion consistent with OPLS-AA forcefield. To my
> surprise, the total charge of the it comes out to be -0.400 while it should
> be +1.000. I also generated a topology for acetate ions and it yields an
> overall charge of -1.000 as expected. What is this anomaly for? Can you
> please give me insights on how to assign correct charges to the atoms here?
> Furthermore, the nitrogen atom is assigned to be secondary amine nitrogen
> atom while in principle it should be a quarternary one. Is the topology
> correct? I am uploading the PDB and the acetate.itp files in this mail.
> Kindly help me out here. Has someone used the TPPMKTOP server before? Any
> kind of insights would be hugely appreciated.
>

If you're having a problem with a specific program, you should contact the 
authors of that program.

> TEA pdb:
> https://drive.google.com/file/d/0B7SBnQ5YXQSLRWxLdVhNbU9haVk/view?usp=sharing
>
> TEA.itp:
> https://drive.google.com/file/d/0B7SBnQ5YXQSLd2NDSnR3Rng4UjQ/view?usp=sharing
>

At quick glance, the program appears to be making some guesses based on analogy. 
  Whereas acetate is straightforward (taken from an Asp or Glu side chain), no 
such analog exists for TEA.  So the program is assuming normal aliphatic groups 
and then approximating the NH charges and types based on what it knows, which is 
deficient.  A proper parametrization starting from QM optimization (your 
geometry in the PDB file is very bad), charge calculation, etc. is needed here.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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