AMBER Archive (2009)

Subject: Re: [AMBER] please help me out

From: rpaduri_at_chem.wayne.edu
Date: Thu Mar 12 2009 - 11:37:09 CDT

Dear Bharat,
Your "frcmod" file looks fine to me. The force constants and the bond lengths or
the angles are in the right ranges. If you want to be absolutely sure you can
energy minimize your molecule using any ab-initio methods and manually look at
the bond lengths and angles. In my experience, the parameters you get from the
antechamber are very well in the acceptable ranges. One thing I will suggest is
to make sure your dihedrals are OK (which look fine to me).
Good luck
Sincerely
Raviprasad Aduri

Quoting bharat lakhani <lakhbharat_at_gmail.com>:

> respected sir,
> As you previous told me.I have done all the steps.I run
> the antechamber to
> find out which angle parameters are missing.
>
> *step 1*
>
> antechamber -i pencillinn.pdb -fi pdb -o pencillin.prepin -fo prepi -c bcc
> -s 2
>
> *Step -2*
>
> parmchk -i pencillin.prepin -f prepi -o pencillin.frcmod
>
>
> my pencillin.frcmod file generating these output
>
> *remark goes here
> MASS
>
> BOND
> n -cy 330.60 1.460 same as c3-n
> cy-h2 326.40 1.100 same as c3-h2
> cy-ss 225.80 1.821 same as c3-ss
>
> ANGLE
> c -n -cy 63.900 121.350 same as c -n -c3
> n -cy-h1 49.800 109.320 same as h1-c3-n
> n -cy-c 66.700 111.560 same as c -c3-n
> hn-n -cy 46.000 116.780 same as c3-n -hn
> cy-c -n 67.619 101.125 Calculated with empirical approach
> cy-cy-h2 44.800 115.140 same as cy-cy-hc
> cy-cy-ss 61.100 112.690 same as c3-c3-ss
> h1-cy-c 45.700 113.850 same as c -cy-hc
> n -cy-h2 50.000 108.310 same as h2-c3-n
> n -cy-ss 63.716 111.415 Calculated with empirical approach
> cy-n -c3 64.000 112.620 same as c3-n -c3
> cy-ss-c3 60.600 99.920 same as c3-ss-c3
> h2-cy-ss 42.300 109.750 same as h2-c3-ss
>
> DIHE
> cy-cy-ss-c3 1 0.333 0.000 3.000 same as X
> -c3-ss-X
> n -cy-ss-c3 1 0.333 0.000 3.000 same as X
> -c3-ss-X
> h2-cy-ss-c3 1 0.333 0.000 3.000 same as X
> -c3-ss-X
>
> IMPROPER
>
> NONBON
>
> *
> So these are the parameters which are missing in my complex.Are they
> correct.
> or i have to validate these parameters can i incorporate these
> parameters.What will be the my next step:
>
>
> On Mon, Mar 9, 2009 at 3:35 PM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
>
> > 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
> > cost).
> > - 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
> > manually.
> >
> > (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 <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
>

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