AMBER Archive (2009)

Subject: Re: [AMBER] please help me out

From: FyD (
Date: Mon Mar 09 2009 - 05:05:06 CDT

Dear bharat lakhani,

> 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

ok I better understand your needs now: You need (i) to derive the
atomic charges, (ii) to determine the force field (FF) atom types, and
(iii) find the missing FF parameters (if any) for your molecules:

(i) To get the charges, you can follow different approaches.
You could use the following plan:
- You get optimized structures by quantum mechanics (QM).
You need a QM program for that: Among the numerous possibilities:
Gaussian, PC-GAMESS or GAMESS-US (the last twos are provided at no
- You compute molecular electrostatic potential (MEP).
- You fit the charges to the MEP.
You can use the R.E.D. tools or Antechamber for that.

If you decide to use the R.E.D. tools, Ante_R.E.D. will generate for
you inputs for the geometry optimization step, and R.E.D. will allow
you to compute the charges for all your molecules in a single
multi-molecule approach.

(ii) you need to decide which FF you want to use. If you decide to use
GAFF, Antechamber will generate the FF atom types for GAFF and find
the missing FF parameters. For other FF, you will have to do the job

(iii) you use LEaP to load the FF libraries and generate the
prmtop/prmcrd files. LEaP will tell you which FF parameter is missing.

I hope this helps. A lot of work... I suggest you to proceed step by
step taking a small molecule as a model first.

regards, Francois

> On Mon, Mar 9, 2009 at 1:40 PM, FyD <> 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

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