Re: [AMBER] please help me out

From: FyD <>
Date: Mon, 09 Mar 2009 09:10:08 +0100

Dear bharat lakhani,

> As You told me previously that in which sturctures u
> have sulphru and chlorine.i mentioned those structures previously and now i
> am again sending you.But i did get any reply from your side.

Yes sorry. This is difficult to answer you because one needs to work
on the structures to see the error messages & missing FF parameters.

> please help me
> out sir.In my structures there are sulfa drugs like sulfanilamide,pencillin
> g,sulfathiazole,pencillin v,Sulfamethoxazole,Pencillin V and the structure
> which have chlorine Chlorpropamide,Tigecycline,Aureomycin I am looking for
> these above force field parameters

Did you already get the atomic charges for those molecules ?
You did not talk about the charges; only about FF parameters...

Did you load your structures in LEaP, and what are the missing FF parameters ?

I think you need to generate your own charges + the missing FF parameters.
* optimized by QM all your structures
* run R.E.D. or Antechamber to get the charges // FF parameters
* run LEaP to save the prmtop/prmcrd files for all your structures.

I am not sure I help you a lot here...

regards, Francois

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Received on Wed Mar 11 2009 - 01:07:11 PDT
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