From: Shoresh Shafei (s.shafei_at_gmail.com)
Date: Thu Jan 28 2016 - 06:52:10 CST

Hi Peter,
Thank you for your response.
I want to add proton, relax the system and then use the pdb snapshots for some quantum chemistry calculations. A sample pdb file contain:

CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 O4 FAD X 470 43.501 42.633 45.794 1.00 0.00 O
ATOM 2 C4 FAD X 470 43.306 41.569 46.281 1.00 0.00 C
ATOM 3 N3 FAD X 470 44.117 41.265 47.336 1.00 0.00 N
ATOM 4 H12 FAD X 470 44.768 41.915 47.755 1.00 0.00 H
ATOM 5 C2 FAD X 470 43.998 40.067 47.943 1.00 0.00 C
ATOM 6 O2 FAD X 470 44.590 39.870 48.988 1.00 0.00 O
ATOM 7 N1 FAD X 470 43.009 39.114 47.519 1.00 0.00 N
ATOM 8 C10 FAD X 470 42.216 39.371 46.498 1.00 0.00 C
ATOM 9 C4A FAD X 470 42.312 40.683 45.888 1.00 0.00 C
ATOM 10 N5 FAD X 470 41.570 41.007 44.746 1.00 0.00 N
ATOM 11 H13 FAD X 470 41.834 41.822 44.208 1.00 0.00 H
ATOM 12 C5A FAD X 470 40.646 40.028 44.235 1.00 0.00 C
ATOM 13 C6 FAD X 470 39.963 40.355 43.049 1.00 0.00 C
ATOM 14 H30 FAD X 470 40.093 41.318 42.563 1.00 0.00 H
ATOM 15 C7 FAD X 470 38.999 39.497 42.588 1.00 0.00 C
ATOM 16 C7M FAD X 470 38.217 39.854 41.320 1.00 0.00 C
ATOM 17 H14 FAD X 470 37.153 40.041 41.485 1.00 0.00 H
ATOM 18 H15 FAD X 470 38.649 40.772 40.916 1.00 0.00 H
ATOM 19 H16 FAD X 470 38.288 38.957 40.702 1.00 0.00 H
ATOM 20 C8 FAD X 470 38.718 38.285 43.276 1.00 0.00 C
ATOM 21 C8M FAD X 470 37.712 37.222 42.783 1.00 0.00 C
ATOM 22 H17 FAD X 470 37.539 37.196 41.705 1.00 0.00 H
ATOM 23 H18 FAD X 470 38.183 36.239 42.859 1.00 0.00 H
ATOM 24 H19 FAD X 470 36.784 37.135 43.352 1.00 0.00 H
ATOM 25 C9 FAD X 470 39.467 37.977 44.408 1.00 0.00 C
ATOM 26 H31 FAD X 470 39.201 37.034 44.878 1.00 0.00 H
ATOM 27 C9A FAD X 470 40.436 38.823 44.922 1.00 0.00 C
ATOM 28 N10 FAD X 470 41.220 38.473 46.077 1.00 0.00 N
ATOM 29 C1* FAD X 470 40.991 37.261 46.820 1.00 0.00 C
ATOM 30 H20 FAD X 470 41.990 36.873 47.026 1.00 0.00 H
ATOM 31 H21 FAD X 470 40.657 36.423 46.205 1.00 0.00 H
ATOM 32 N91 FAD X 470 42.624 34.867 50.234 1.00 0.00 N
ATOM 33 C81 FAD X 470 41.344 34.363 50.094 1.00 0.00 C
ATOM 34 H32 FAD X 470 40.756 34.206 50.994 1.00 0.00 H
ATOM 35 N71 FAD X 470 40.835 34.080 48.801 1.00 0.00 N
ATOM 36 C51 FAD X 470 42.010 34.316 48.062 1.00 0.00 C
ATOM 37 C61 FAD X 470 42.332 34.194 46.643 1.00 0.00 C
ATOM 38 N61 FAD X 470 41.525 33.658 45.785 1.00 0.00 N
ATOM 39 H9 FAD X 470 41.180 32.736 46.042 1.00 0.00 H
ATOM 40 H10 FAD X 470 41.961 33.440 44.891 1.00 0.00 H
ATOM 41 N11 FAD X 470 43.415 34.580 46.112 1.00 0.00 N
ATOM 42 C21 FAD X 470 44.381 35.027 46.964 1.00 0.00 C
ATOM 43 H11 FAD X 470 45.293 35.411 46.514 1.00 0.00 H
ATOM 44 N31 FAD X 470 44.302 35.193 48.350 1.00 0.00 N
ATOM 45 C41 FAD X 470 43.082 34.748 48.900 1.00 0.00 C
ATOM 46 N1 CPD X 471 38.015 28.575 44.118 1.00 0.00 N
ATOM 47 C2 CPD X 471 38.169 28.499 45.445 1.00 0.00 C
ATOM 48 O2 CPD X 471 37.980 27.465 46.038 1.00 0.00 O
ATOM 49 N3 CPD X 471 38.680 29.601 46.033 1.00 0.00 N
ATOM 50 C4 CPD X 471 39.130 30.776 45.549 1.00 0.00 C
ATOM 51 O4 CPD X 471 39.684 31.500 46.362 1.00 0.00 O
ATOM 52 C5 CPD X 471 38.958 31.061 44.066 1.00 0.00 C
ATOM 53 C5M CPD X 471 40.237 31.321 43.247 1.00 0.00 C
ATOM 54 H10 CPD X 471 40.266 30.710 42.342 1.00 0.00 H
ATOM 55 H11 CPD X 471 40.476 32.382 43.140 1.00 0.00 H
ATOM 56 H12 CPD X 471 41.123 30.940 43.759 1.00 0.00 H
ATOM 57 C6 CPD X 471 38.100 29.930 43.448 1.00 0.00 C
ATOM 58 H13 CPD X 471 38.500 29.724 42.453 1.00 0.00 H
ATOM 59 C6' CPD X 471 36.844 30.896 43.271 1.00 0.00 C
ATOM 60 N1' CPD X 471 35.627 30.731 44.205 1.00 0.00 N
ATOM 61 C2' CPD X 471 35.504 31.550 45.321 1.00 0.00 C
ATOM 62 O2' CPD X 471 34.632 31.452 46.114 1.00 0.00 O
ATOM 63 N3' CPD X 471 36.342 32.519 45.492 1.00 0.00 N
ATOM 64 C4' CPD X 471 37.379 32.923 44.821 1.00 0.00 C
ATOM 65 O4' CPD X 471 37.965 33.957 45.167 1.00 0.00 O
ATOM 66 C5' CPD X 471 37.791 32.065 43.653 1.00 0.00 C
ATOM 67 C5N CPD X 471 38.012 32.901 42.327 1.00 0.00 C
ATOM 68 H22 CPD X 471 38.114 32.274 41.439 1.00 0.00 H
ATOM 69 H23 CPD X 471 37.111 33.489 42.142 1.00 0.00 H
ATOM 70 H24 CPD X 471 38.806 33.647 42.386 1.00 0.00 H
ATOM 71 H21 CPD X 471 36.041 33.252 46.115 1.00 0.00 H
ATOM 72 H25 CPD X 471 36.400 30.870 42.274 1.00 0.00 H
ATOM 73 H9 CPD X 471 38.869 29.482 47.017 1.00 0.00 H
ATOM 74 H FAD X 470 43.166 34.320 50.872 1.00 0.00 H
ATOM 75 H FAD X 470 40.378 37.271 47.610 1.00 0.00 H
END

where I want to add protons to C1*, N91, N1 and N1’ atoms. Molefacture should work and I wonder if you can you kindly provide a more detailed script?

Best,
Sho

> On Jan 28, 2016, at 1:00 AM, Peter Freddolino <petefred_at_umich.edu> wrote:
>
> Hi Sho,
> This really depends on what you want to do with the structures afterwards. If you’re going to use them for any kind of simulation, you’re probably best off using the toolchain appropriate for system preparation for your simulations (e.g., psfgen for namd). If you really just want to add the proton and do nothing else, you can call molefacture from the scripting interface too, but it is not for the faint of heart. You’d need to do
> package require molefacture
> to load it up, and then call ::Molefacture::molefacture_gui_aux to initialize the molecule and ::Molefacture::add_hydrogen (both with appropriate arguments — the source code is at least somewhat decently documented in these portions) to add the hydrogen, and then save the resulting structure.
> There are also easier ways, depending on some details of your problem; for example, you could write your own script that adds two hydrogens to a pdb file, and then opens up vmd and moves them to appropriate places. But we could provide more useful help if you gave more details on what you’re going to use the files for.
>
> Best,
> Peter
>
>
>> On Jan 27, 2016, at 11:15 AM, Shoresh Shafei <s.shafei_at_gmail.com> wrote:
>>
>> Hi,
>>
>> I have 200 pruned pdb files in which I would like to add a hydrogen to atom A and one to atom B. I know that for a pdb file, this can be done using molefacture, however I wonder if there is a script to automate this process for 200 pdb files.
>>
>> Best
>> Sho
>>
>