AMBER Archive (2009)

Subject: Re: [AMBER] please help me out

From: bharat lakhani (lakhbharat_at_gmail.com)
Date: Thu Mar 12 2009 - 01:04:00 CDT

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
>>>
>>
>
>
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