Dear all amber users,
I have tried what Mr. Francois told me last week, i drew my own ligand by using symyx draw tool (output file is .mol in 2 dimensions), and then i have converted the .mol file into 3D structure by openbabel program. So, i want to start the minimization with 3D ligand that i have created before (I have erased the connect in my ligand file). I just followed the instruction in antechamber tutorial by Ross Walker and Sishi Tang to create parameter and coordinate files for ligand. First, i want to use command reduce to add hydrogen into my ligand, but there were no hydrogen was added at all, here is my ligand file:
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.0
HETATM 1 C LIG 1 10.297 -4.293 4.606 1.00 0.00 C
HETATM 2 C LIG 1 10.551 -2.679 2.886 1.00 0.00 C
HETATM 3 C LIG 1 9.798 -3.439 3.697 1.00 0.00 C
HETATM 4 C LIG 1 6.078 -1.659 1.804 1.00 0.00 C
HETATM 5 C LIG 1 9.466 -5.014 5.376 1.00 0.00 C
HETATM 6 C LIG 1 4.739 -1.592 1.735 1.00 0.00 C
HETATM 7 C LIG 1 9.964 -1.852 2.005 1.00 0.00 C
HETATM 8 N LIG 1 8.669 -1.788 1.938 1.00 0.00 N
HETATM 9 C LIG 1 8.102 -0.988 1.086 1.00 0.00 C
HETATM 10 N LIG 1 6.806 -0.924 1.019 1.00 0.00 N
HETATM 11 O LIG 1 10.653 -1.157 1.263 1.00 0.00 O
HETATM 12 C LIG 1 7.886 -2.578 2.782 1.00 0.00 C
HETATM 13 C LIG 1 2.362 -3.900 4.197 1.00 0.00 C
HETATM 14 C LIG 1 6.547 -2.512 2.712 1.00 0.00 C
HETATM 15 C LIG 1 5.794 -3.272 3.524 1.00 0.00 C
HETATM 16 C LIG 1 3.701 -3.966 4.266 1.00 0.00 C
HETATM 17 C LIG 1 4.454 -3.206 3.454 1.00 0.00 C
HETATM 18 C LIG 1 8.911 -0.170 0.214 1.00 0.00 C
HETATM 19 C LIG 1 8.337 0.639 -0.648 1.00 0.00 C
HETATM 20 C LIG 1 9.147 1.457 -1.520 1.00 0.00 C
HETATM 21 C LIG 1 6.634 3.177 -3.351 1.00 0.00 C
HETATM 22 C LIG 1 7.387 3.937 -4.162 1.00 0.00 C
HETATM 23 C LIG 1 8.727 3.871 -4.093 1.00 0.00 C
HETATM 24 S LIG 1 9.720 4.874 -5.164 1.00 0.00 S
HETATM 25 C LIG 1 9.313 3.044 -3.212 1.00 0.00 C
HETATM 26 C LIG 1 8.561 2.283 -2.401 1.00 0.00 C
HETATM 27 O LIG 1 10.590 5.800 -4.319 1.00 0.00 O
HETATM 28 O LIG 1 10.635 3.996 -6.013 1.00 0.00 O
HETATM 29 N LIG 1 8.676 5.844 -6.196 1.00 0.00 N
HETATM 30 H LIG 1 11.318 -4.394 4.713 1.00 0.00 H
HETATM 31 H LIG 1 8.772 -3.363 3.617 1.00 0.00 H
HETATM 32 H LIG 1 9.513 -5.720 6.128 1.00 0.00 H
HETATM 33 H LIG 1 3.806 -1.290 1.413 1.00 0.00 H
HETATM 34 H LIG 1 1.339 -3.992 4.297 1.00 0.00 H
HETATM 35 H LIG 1 6.096 -1.876 2.036 1.00 0.00 H
HETATM 36 H LIG 1 6.244 -3.908 4.201 1.00 0.00 H
HETATM 37 H LIG 1 4.152 -4.602 4.943 1.00 0.00 H
HETATM 38 H LIG 1 4.003 -2.570 2.778 1.00 0.00 H
HETATM 39 H LIG 1 9.941 -0.221 0.267 1.00 0.00 H
HETATM 40 H LIG 1 7.308 0.690 -0.701 1.00 0.00 H
HETATM 41 H LIG 1 5.607 3.110 -3.279 1.00 0.00 H
HETATM 42 H LIG 1 6.937 4.573 -4.839 1.00 0.00 H
HETATM 43 H LIG 1 10.343 2.993 -3.159 1.00 0.00 H
HETATM 44 H LIG 1 7.531 2.335 -2.454 1.00 0.00 H
HETATM 45 H LIG 1 8.092 5.229 -6.763 1.00 0.00 H
HETATM 46 H LIG 1 9.236 6.450 -6.795 1.00 0.00 H
TER
END
and the output file is:
USER MOD reduce.3.14.080821 H: found=17, std=0, add=0, rem=0, adj=0
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.0
HETATM 1 C LIG 1 10.297 -4.293 4.606 1.00 0.00 C
HETATM 2 C LIG 1 10.551 -2.679 2.886 1.00 0.00 C
HETATM 3 C LIG 1 9.798 -3.439 3.697 1.00 0.00 C
HETATM 4 C LIG 1 6.078 -1.659 1.804 1.00 0.00 C
HETATM 5 C LIG 1 9.466 -5.014 5.376 1.00 0.00 C
HETATM 6 C LIG 1 4.739 -1.592 1.735 1.00 0.00 C
HETATM 7 C LIG 1 9.964 -1.852 2.005 1.00 0.00 C
HETATM 8 N LIG 1 8.669 -1.788 1.938 1.00 0.00 N
HETATM 9 C LIG 1 8.102 -0.988 1.086 1.00 0.00 C
HETATM 10 N LIG 1 6.806 -0.924 1.019 1.00 0.00 N
HETATM 11 O LIG 1 10.653 -1.157 1.263 1.00 0.00 O
HETATM 12 C LIG 1 7.886 -2.578 2.782 1.00 0.00 C
HETATM 13 C LIG 1 2.362 -3.900 4.197 1.00 0.00 C
HETATM 14 C LIG 1 6.547 -2.512 2.712 1.00 0.00 C
HETATM 15 C LIG 1 5.794 -3.272 3.524 1.00 0.00 C
HETATM 16 C LIG 1 3.701 -3.966 4.266 1.00 0.00 C
HETATM 17 C LIG 1 4.454 -3.206 3.454 1.00 0.00 C
HETATM 18 C LIG 1 8.911 -0.170 0.214 1.00 0.00 C
HETATM 19 C LIG 1 8.337 0.639 -0.648 1.00 0.00 C
HETATM 20 C LIG 1 9.147 1.457 -1.520 1.00 0.00 C
HETATM 21 C LIG 1 6.634 3.177 -3.351 1.00 0.00 C
HETATM 22 C LIG 1 7.387 3.937 -4.162 1.00 0.00 C
HETATM 23 C LIG 1 8.727 3.871 -4.093 1.00 0.00 C
HETATM 24 S LIG 1 9.720 4.874 -5.164 1.00 0.00 S
HETATM 25 C LIG 1 9.313 3.044 -3.212 1.00 0.00 C
HETATM 26 C LIG 1 8.561 2.283 -2.401 1.00 0.00 C
HETATM 27 O LIG 1 10.590 5.800 -4.319 1.00 0.00 O
HETATM 28 O LIG 1 10.635 3.996 -6.013 1.00 0.00 O
HETATM 29 N LIG 1 8.676 5.844 -6.196 1.00 0.00 N
HETATM 30 H LIG 1 11.318 -4.394 4.713 1.00 0.00 H
HETATM 31 H LIG 1 8.772 -3.363 3.617 1.00 0.00 H
HETATM 32 H LIG 1 9.513 -5.720 6.128 1.00 0.00 H
HETATM 33 H LIG 1 3.806 -1.290 1.413 1.00 0.00 H
HETATM 34 H LIG 1 1.339 -3.992 4.297 1.00 0.00 H
HETATM 35 H LIG 1 6.096 -1.876 2.036 1.00 0.00 H
HETATM 36 H LIG 1 6.244 -3.908 4.201 1.00 0.00 H
HETATM 37 H LIG 1 4.152 -4.602 4.943 1.00 0.00 H
HETATM 38 H LIG 1 4.003 -2.570 2.778 1.00 0.00 H
HETATM 39 H LIG 1 9.941 -0.221 0.267 1.00 0.00 H
HETATM 40 H LIG 1 7.308 0.690 -0.701 1.00 0.00 H
HETATM 41 H LIG 1 5.607 3.110 -3.279 1.00 0.00 H
HETATM 42 H LIG 1 6.937 4.573 -4.839 1.00 0.00 H
HETATM 43 H LIG 1 10.343 2.993 -3.159 1.00 0.00 H
HETATM 44 H LIG 1 7.531 2.335 -2.454 1.00 0.00 H
HETATM 45 H LIG 1 8.092 5.229 -6.763 1.00 0.00 H
HETATM 46 H LIG 1 9.236 6.450 -6.795 1.00 0.00 H
TER
END
My question is, why antechamber did not add hydrogen in my ligand? and why i could not converted the .pdb file into .mol2 by antechamber? here is the respond of antechamber:
Warning: the assigned bond typesmay be wrong, please:
1. double check the structure (the connectivity) and/or
2. adjust atom valence penalty parameters in APS.DAT, and/or
3. increase PSCUTOFF in define.h and recompile bondtype.c
be cautious, use a large value of PSCUTOFF (>100) will significantly increase the computation time
please help me why it could not work to create .mol2 file by using antechamber..
Best regards, Aditya Setiajid
________________________________
From: FyD <fyd.q4md-forcefieldtools.org>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, February 22, 2012 4:11 PM
Subject: Re: [AMBER] Using Antechamber in order to make prmtop and inpcrd
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 Mon Feb 27 2012 - 00:00:01 PST
