Dear Francois,
Ok i will try later.. i will ask again if i face a problem again. thx sir..
Sent from my iPad
On 22 Feb 2012, at 16:11, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Aditya Setiajid,
>
> As I told you you drew a structure and generated a mol file for the
> corresponding molecule; this likely means you generated a structure in
> 2 dimensions; i.e. Z coordinates = 0.0.
>
> HETATM 1 C LIG 1 11.676 -12.169 0.000 1.00 0.00 C
> ^^^^^^
> As you can see, Z coordinates = 0
> I am not sure "reduce" can add hydrogens based on a molecule built in
> 2 dimensions.
>
> I might be wrong but I think you need to create a structure in 3 dimensions...
> You can using xLEaP & its drawing mode for that...
>
> regards, Francois
>
>
>> I have tried to create prmtop and inpcrd files from pdb which i drew
>> by my self (i drew the structure by symyx draw, the output file
>> is.mol, and then i converted .mol to .pdb using openbabel program)
>> After that, i want to add hydrogen by using command: reduce file.pbd
>>> file_h.pdb , here is the output file:
>> USER MOD reduce.3.14.080821 H: found=0, std=0, add=0, rem=0, adj=0
>> COMPND UNNAMED
>> AUTHOR GENERATED BY OPEN BABEL 2.3.0
>> HETATM 1 C LIG 1 11.676 -12.169 0.000 1.00
>> 0.00 C
>> HETATM 2 C LIG 1 13.106 -12.169 0.000 1.00
>> 0.00 C
>> HETATM 3 C LIG 1 12.392 -11.756 0.000 1.00
>> 0.00 C
>> HETATM 4 C LIG 1 13.106 -12.996 0.000 1.00
>> 0.00 C
>> HETATM 5 C LIG 1 11.676 -13.000 0.000 1.00
>> 0.00 C
>> HETATM 6 C LIG 1 12.394 -13.409 0.000 1.00
>> 0.00 C
>> HETATM 7 C LIG 1 13.822 -11.756 0.000 1.00
>> 0.00 C
>> HETATM 8 N LIG 1 14.538 -12.169 0.000 1.00
>> 0.00 N
>> HETATM 9 C LIG 1 14.538 -12.996 0.000 1.00
>> 0.00 C
>> HETATM 10 N LIG 1 13.822 -13.410 0.000 1.00
>> 0.00 N
>> HETATM 11 O LIG 1 13.822 -10.929 0.000 1.00
>> 0.00 O
>> HETATM 12 C LIG 1 15.255 -11.756 0.000 1.00
>> 0.00 C
>> HETATM 13 C LIG 1 15.255 -10.929 0.000 1.00
>> 0.00 C
>> HETATM 14 C LIG 1 15.971 -12.169 0.000 1.00
>> 0.00 C
>> HETATM 15 C LIG 1 16.687 -11.756 0.000 1.00
>> 0.00 C
>> HETATM 16 C LIG 1 15.971 -10.515 0.000 1.00
>> 0.00 C
>> HETATM 17 C LIG 1 16.687 -10.929 0.000 1.00
>> 0.00 C
>> HETATM 18 C LIG 1 15.255 -13.410 0.000 1.00
>> 0.00 C
>> HETATM 19 C LIG 1 15.971 -12.996 0.000 1.00
>> 0.00 C
>> HETATM 20 C LIG 1 16.687 -13.410 0.000 1.00
>> 0.00 C
>> HETATM 21 C LIG 1 17.403 -12.996 0.000 1.00
>> 0.00 C
>> HETATM 22 C LIG 1 18.119 -13.410 0.000 1.00
>> 0.00 C
>> HETATM 23 C LIG 1 18.119 -14.236 0.000 1.00
>> 0.00 C
>> HETATM 24 S LIG 1 18.836 -14.650 0.000 1.00
>> 0.00 S
>> HETATM 25 C LIG 1 17.403 -14.650 0.000 1.00
>> 0.00 C
>> HETATM 26 C LIG 1 16.687 -14.236 0.000 1.00
>> 0.00 C
>> HETATM 27 O LIG 1 19.552 -14.236 0.000 1.00
>> 0.00 O
>> HETATM 28 O LIG 1 18.836 -15.477 0.000 1.00
>> 0.00 O
>> HETATM 29 N LIG 1 19.552 -15.063 0.000 1.00
>> 0.00 N
>> TER
>> END
>>
>> Why it was different from the sustiva/efavirenz output file which
>> was from antechamber tutorial by Ross Walker and Sishi Tang? in my
>> output file, there were no NEW Hydrogen? is it ok or not if there
>> were no NEW hydrogen?
>>
>> Here is the file from the antechamber tutorial:
>>
>>
>>
>> USER MOD reduce.3.14.080821 H: found=0, std=0, add=9, rem=0, adj=0
>> REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EFZ A 999
>> HETATM 7759 CL EFZ A 999 -4.685 -32.725 25.222 1.00
>> 50.93 CL
>> HETATM 7760 F1 EFZ A 999 -0.755 -36.632 25.697 1.00
>> 62.80 F
>> HETATM 7761 F2 EFZ A 999 1.078 -37.043 24.672 1.00
>> 70.73 F
>> HETATM 7762 F3 EFZ A 999 -0.784 -37.177 23.626 1.00
>> 75.12 F
>> HETATM 7763 O1 EFZ A 999 1.524 -34.934 20.910 1.00
>> 73.73 O
>> HETATM 7764 O2 EFZ A 999 0.989 -34.880 23.058 1.00
>> 73.24 O
>> HETATM 7765 N EFZ A 999 -0.681 -34.971 21.434 1.00
>> 71.12 N
>> HETATM 7766 C1 EFZ A 999 -1.662 -34.414 22.313 1.00
>> 71.29 C
>> HETATM 7767 C2 EFZ A 999 -2.915 -33.947 21.843 1.00
>> 72.17 C
>> HETATM 7768 C3 EFZ A 999 -3.838 -33.423 22.771 1.00
>> 71.25 C
>> HETATM 7769 C4 EFZ A 999 -3.533 -33.373 24.119 1.00
>> 63.88 C
>> HETATM 7770 C5 EFZ A 999 -2.310 -33.829 24.593 1.00
>> 63.40 C
>> HETATM 7771 C6 EFZ A 999 -1.386 -34.378 23.681 1.00
>> 68.96 C
>> HETATM 7772 C7 EFZ A 999 -0.002 -34.957 24.144 1.00
>> 71.35 C
>> HETATM 7773 C8 EFZ A 999 0.552 -34.236 25.315 1.00
>> 75.97 C
>> HETATM 7774 C9 EFZ A 999 0.985 -33.657 26.241 1.00
>> 81.31 C
>> HETATM 7775 C10 EFZ A 999 1.605 -32.802 27.586 1.00
>> 80.51 C
>> HETATM 7776 C11 EFZ A 999 2.808 -33.083 27.639 1.00
>> 83.59 C
>> HETATM 7777 C12 EFZ A 999 2.404 -31.980 27.123 1.00
>> 79.58 C
>> HETATM 7778 C13 EFZ A 999 -0.121 -36.472 24.539 1.00
>> 72.76 C
>> HETATM 7779 C14 EFZ A 999 0.665 -34.932 21.725 1.00
>> 70.58 C
>> HETATM 0 H122 EFZ A 999 2.472 -31.798 26.040 1.00
>> 79.58 H new
>> HETATM 0 H121 EFZ A 999 2.585 -31.017 27.623 1.00
>> 79.58 H new
>> HETATM 0 H112 EFZ A 999 3.348 -33.100 28.597 1.00
>> 83.59 H new
>> HETATM 0 H111 EFZ A 999 3.235 -33.882 27.015 1.00
>> 83.59 H new
>> HETATM 0 H101 EFZ A 999 0.784 -32.761 28.317 1.00
>> 80.51 H new
>> HETATM 0 HN EFZ A 999 -0.981 -35.402 20.583 1.00
>> 71.12 H new
>> HETATM 0 H5 EFZ A 999 -2.066 -33.763 25.664 1.00
>> 63.40 H new
>> HETATM 0 H3 EFZ A 999 -4.811 -33.050 22.419 1.00
>> 71.25 H new
>> HETATM 0 H2 EFZ A 999 -3.163 -33.993 20.772 1.00
>> 72.17 H new
>> TER
>> END
>>
>>
>> Regards, Aditya Setiajid
>>
>>
>> ________________________________
>> From: FyD <fyd.q4md-forcefieldtools.org>
>> To: AMBER Mailing List <amber.ambermd.org>
>> Sent: Wednesday, February 22, 2012 1:10 PM
>> Subject: Re: [AMBER] Using Antechamber in order to make prmtop and inpcrd
>>
>> Dear Aditya Setiajid,
>>
>> I wonder if you drew your molecule and consequently generated a
>> structure in 2 dimensions (2D)... I would construct a structure in 3D
>> using xLEaP from AmberTools, using Javaapplet & Jmol, using whatever
>> existing tool etc...
>>
>> for LEaP, you should generate a PDB file format for your input PDB
>> molecule. I do not think LEaP does understand the mol fle format.
>>
>> regards, Francois
>>
>>
>>> Hi, i'm newbie in using amber suite.. now i'm using amber 11..
>>>
>>> I want to ask how to make prmtop and inpcrd for the ligand that
>>> drawn by our self? I drawn the ligand using symyx draw, the output
>>> file is .mol, here is the file:
>>>
>>> SMMXDraw02141214502D
>>>
>>> 29 32 0 0 0 0 0 0 0 0999 V2000
>>> 11.6762 -12.1694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 13.1058 -12.1690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 12.3924 -11.7562 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 13.1058 -12.9960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 11.6762 -12.9997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 12.3942 -13.4087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 13.8220 -11.7555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 14.5382 -12.1690 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0
>>> 14.5382 -12.9960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 13.8220 -13.4095 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
>>> 13.8220 -10.9285 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>> 15.2545 -11.7555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 15.2545 -10.9285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 15.9707 -12.1690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 16.6869 -11.7555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 15.9707 -10.5149 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 16.6869 -10.9285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 15.2545 -13.4095 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 15.9707 -12.9960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 16.6869 -13.4095 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 17.4031 -12.9960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 18.1193 -13.4095 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 18.1193 -14.2365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 18.8355 -14.6500 0.0000 S 0 0 3 0 0 0 0 0 0 0 0 0
>>> 17.4031 -14.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 16.6869 -14.2365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>> 19.5518 -14.2365 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>> 18.8355 -15.4770 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>> 19.5518 -15.0635 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
>>> 6 4 1 0 0 0 0
>>> 5 6 2 0 0 0 0
>>> 2 3 1 0 0 0 0
>>> 1 5 1 0 0 0 0
>>> 4 2 2 0 0 0 0
>>> 3 1 2 0 0 0 0
>>> 2 7 1 0 0 0 0
>>> 7 8 1 0 0 0 0
>>> 8 9 1 0 0 0 0
>>> 9 10 2 0 0 0 0
>>> 4 10 1 0 0 0 0
>>> 7 11 2 0 0 0 0
>>> 8 12 1 0 0 0 0
>>> 12 13 2 0 0 0 0
>>> 12 14 1 0 0 0 0
>>> 14 15 2 0 0 0 0
>>> 13 16 1 0 0 0 0
>>> 16 17 2 0 0 0 0
>>> 9 18 1 0 0 0 0
>>> 18 19 2 0 0 0 0
>>> 19 20 1 0 0 0 0
>>> 20 21 2 0 0 0 0
>>> 21 22 1 0 0 0 0
>>> 22 23 2 0 0 0 0
>>> 23 24 1 0 0 0 0
>>> 23 25 1 0 0 0 0
>>> 25 26 2 0 0 0 0
>>> 24 27 2 0 0 0 0
>>> 24 28 2 0 0 0 0
>>> 24 29 1 0 0 0 0
>>> 17 15 1 0 0 0 0
>>> 20 26 1 0 0 0 0
>>> M END
>>>
>>> when i want to use command reduce to add all the hydrogen atoms to
>>> the mole file, why it was different from the antechamber tutorial by
>>> ross walker and sishi tang? is it different when we want to use
>>> ligand file between file that we drawn by ourself using symyx draw
>>> and file from www.pdb.org?
>
>
> F.-Y. Dupradeau
> ---
> http://q4md-forcefieldtools.org/FyD/
>
>
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Received on Wed Feb 22 2012 - 04:00:02 PST
