AMBER Archive (2009)

Subject: Re: [AMBER] please help me out

From: bharat lakhani (lakhbharat_at_gmail.com)
Date: Mon Mar 09 2009 - 03:43:08 CDT

Sir,i dont know how to run QM can you tell me how can i run QM for these
ligands if you have some tutorial regarding this QM please let me know

On Mon, Mar 9, 2009 at 1:40 PM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:

> 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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber