MD of small molecules

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MD of small molecules

sadia tanweer
I worked on small compounds,nitrophenol, but after applying amber  forcefeild the compound got disoriented.how to solve this problem?
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Re: MD of small molecules

agilemolecule
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Amber has no parameters for nitrophenol. What exactly did you do?
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Re: MD of small molecules

sadia tanweer

I am working on interaction of beta cyclodextrin with different small compounds.When I performed the MD of nitrophenol with beta cyclodextrin,by freezing beta-cyclodextrin molecule,the nitrophenol deformed.Please help me in sorting out this problem.

On Apr 4, 2015 10:16 AM, "agilemolecule [via Forum]" <[hidden email]> wrote:
Amber has no parameters for nitrophenol. What exactly did you do?


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Re: MD of small molecules

agilemolecule
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Probably you need more precise parameters than those are default in the ad hoc model.
Look in the AMBER papers how to develop a force field.
Examples of how to do this in Ascalaph are in pages:
http://www.biomolecular-modeling.com/Ascalaph/Documents/Small-Molecule-Model.html
http://www.biomolecular-modeling.com/Ascalaph/Documents/Tutor-Force-Field.html