[gmx-users] Regarding generating itp file.

[Justin Lemkul]

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On 12/11/15 8:02 AM, Raju Lunkad wrote:
> Dear,
>
> In  calcium oxalate monohydrate the charges are,
> Type      charge
> Ca           2
> C             0.992
> O(oxal..)  -0.996
> O(water)  -0.773
> H             0.3665
>
> calcium oxalate monohydrate having two type of bonding which are,
> Ox1 oxalate bounded with calcium only
> and Ox2, oxalate bounded with calcium and oxygen.So, Kindly help me for
> generating itp file for these type of interactions.
>

If you want bonds between those atom types (probably not necessary given the 
strong electrostatic interaction between the carboxylate and Ca2+) you'll have 
to do some sort of QM calculation to get the vibrational frequency and 
subsequently the force constant.

-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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