Dear 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?
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Received on Tue Feb 21 2012 - 23:00:01 PST
