Dear Anselm,
Thanks a lot, you are right the pdb should have something.
I found a mistake in the pdb in case of 1TSRB_R273H+.
Because I used PyMOL for mutation some TER added in different places and one of them in protein so affect the chart calculation in protein.
This is not the case in 1TSRB_R273H, because I did that one month ago and I modified the pdb before using leap at that time but I forgot to do the same yesterday before calculating the charge by tleap
So now its okay and the total charge became -38 like the wild type case
You are
Best regards,
Mohamed Marzouk Sobeh
Ph.D student at Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
T.A Physics department,Ain Shams University, Cairo, Egypt.
Emails:
mohamed_marzouk.sci.asu.edu.eg
marzouk.aa.m.titech.ac.jp
marzouk_biophysics.yahoo.com
mohamedmarzoukphysics.gmail.com
Mob. and WhatsApp.:
+81 070-4070-9549
+2 01061417414
> On Reiwa 3 Nov 27, at 3:01, Dr. Anselm Horn <anselm.horn.fau.de> wrote:
>
> Mohamed,
>
> I'm lost here: this part of your pdb file looks ok to me.
> Are you sure that you did not change anything else in the pdb files?
>
> Since you seem to have nucleic acid residues in your file, try the
> following: Reduce your system in the pdb file to just the protein, run
> leap again with an input file (reproducibility) and see whether the
> problem still remains. If so, reduce it further to just a single chain
> holding your HIS with different protonation state, and retry.
>
> Good luck.
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
> Am 26.11.2021 um 18:09 schrieb mohamed marzouk:
>> Dr Anselm
>>
>> Case one His
>> 1TSRB_R273H.pbd
>> ATOM 2764 N HID 181 85.960 54.212 64.853 1.00 0.00 N
>> ATOM 2765 CA HID 181 85.005 54.443 65.910 1.00 0.00 C
>> ATOM 2766 C HID 181 85.528 55.491 66.889 1.00 0.00 C
>> ATOM 2767 O HID 181 86.216 55.109 67.803 1.00 0.00 O
>> ATOM 2768 CB HID 181 84.633 53.096 66.609 1.00 0.00 C
>> ATOM 2769 CG HID 181 83.564 53.187 67.696 1.00 0.00 C
>> ATOM 2770 CD2 HID 181 83.823 53.296 69.066 1.00 0.00 C
>> ATOM 2771 ND1 HID 181 82.202 53.229 67.476 1.00 0.00 N
>> ATOM 2772 CE1 HID 181 81.748 53.355 68.754 1.00 0.00 C
>> ATOM 2773 NE2 HID 181 82.642 53.419 69.778 1.00 0.00 N
>> ATOM 2774 H HID 181 86.934 54.289 65.145 1.00 0.00 H
>> ATOM 2775 HA HID 181 84.127 54.914 65.440 1.00 0.00 H
>> ATOM 2776 2HB HID 181 85.533 52.626 67.057 1.00 0.00 H
>> ATOM 2777 3HB HID 181 84.307 52.332 65.880 1.00 0.00 H
>> ATOM 2778 1HD HID 181 81.683 53.187 66.593 1.00 0.00 H
>> ATOM 2779 2HD HID 181 84.813 53.284 69.506 1.00 0.00 H
>> ATOM 2780 1HE HID 181 80.685 53.405 68.952 1.00 0.00 H
>>
>> Case 2 1TSRB_R273H+.pdb
>> ATOM 2764 N HIP 181 85.792 54.307 64.821 1.00 0.00 N
>> ATOM 2765 CA HIP 181 84.801 54.530 65.851 1.00 0.00 C
>> ATOM 2766 C HIP 181 85.335 55.517 66.886 1.00 0.00 C
>> ATOM 2767 O HIP 181 85.982 55.080 67.806 1.00 0.00 O
>> ATOM 2768 CB HIP 181 84.415 53.142 66.469 1.00 0.00 C
>> ATOM 2769 CG HIP 181 83.344 53.136 67.561 1.00 0.00 C
>> ATOM 2770 CD2 HIP 181 83.579 53.311 68.936 1.00 0.00 C
>> ATOM 2771 ND1 HIP 181 81.981 52.977 67.341 1.00 0.00 N1+
>> ATOM 2772 CE1 HIP 181 81.484 53.150 68.602 1.00 0.00 C
>> ATOM 2773 NE2 HIP 181 82.374 53.333 69.628 1.00 0.00 N
>> ATOM 2774 H HIP 181 86.753 54.367 65.177 1.00 0.00 H
>> ATOM 2775 HA HIP 181 83.943 55.030 65.384 1.00 0.00 H
>> ATOM 2776 2HB HIP 181 85.318 52.643 66.876 1.00 0.00 H
>> ATOM 2777 3HB HIP 181 84.092 52.431 65.685 1.00 0.00 H
>> ATOM 2778 1HD HIP 181 81.497 52.785 66.451 1.00 0.00 H
>> ATOM 2779 2HD HIP 181 84.580 53.409 69.361 1.00 0.00 H
>> ATOM 2780 1HE HIP 181 80.405 53.141 68.770 1.00 0.00 H
>> ATOM 2781 2HE HIP 181 82.190 53.456 70.635 1.00 0.00 H
>>
>> I could not use diff, because I used pymol to mutate the system then relaxation so the position of atoms different
>>
>>
>> Best regards,
>> Mohamed Marzouk Sobeh
>> Ph.D student at Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
>> T.A Physics department,Ain Shams University, Cairo, Egypt.
>> Emails:
>> mohamed_marzouk.sci.asu.edu.eg
>> marzouk.aa.m.titech.ac.jp
>> marzouk_biophysics.yahoo.com
>> mohamedmarzoukphysics.gmail.com
>>
>> Mob. and WhatsApp.:
>> +81 070-4070-9549
>> +2 01061417414
>>
>>
>>
>>
>>
>>> On Reiwa 3 Nov 27, at 2:02, Dr. Anselm Horn <anselm.horn.fau.de> wrote:
>>>
>>> Mohamed,
>>>
>>> ok, so if your leap input is correct, it is most probably a problem with
>>> your input pdb file. Please check that the two pdb files, which you
>>> specify in your leap input, really contain the histidines with the
>>> correct names (maybe you have temporary files there).
>>> Please do a diff between the two input files in the two directories,
>>> which should then yield just this residue as difference and also show
>>> HID and HIP.
>>>
>>> Good luck.
>>>
>>> Anselm
>>>
>>> Bioinformatik | NHR.FAU
>>> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
>>> Germany
>>>
>>>
>>>
>>> Am 26.11.2021 um 17:39 schrieb mohamed marzouk:
>>>> Hello Anselm,
>>>>
>>>> The case of Histidine in form δ-histidine (with residue name in pdb; HID)
>>>>
>>>>> savepdb mol 1TSRB_R273H_dry.pdb
>>>> Writing pdb file: 1TSRB_R273H_dry.pdb
>>>>>
>>>>> charge mol
>>>> Total unperturbed charge: -39.000050
>>>> Total perturbed charge: -39.000050
>>>>>
>>>>> solvatebox mol TIP3PBOX {50 30 30} iso
>>>> Solute vdw bounding box: 74.157 46.691 76.583
>>>> Total bounding box for atom centers: 174.157 174.157 174.157
>>>> (box expansion for 'iso' is 108.1%)
>>>> Solvent unit box: 18.774 18.774 18.774
>>>> The number of boxes: x=10 y=10 z=10
>>>> Adding box at: x=0 y=0 z=0
>>>> Center of solvent box is: 84.484571, 84.484571, 84.484571
>>>>
>>>> The other case, Histidine in form protonated form (HIP)
>>>>
>>>> Loading PDB file: ./1TSRB_R273H+.pdb
>>>> Added missing heavy atom: .R<CLEU 197>.A<OXT 20>
>>>> One sided connection. Residue: default_name missing connect1 atom.
>>>> One sided connection. Residue: DT5 missing connect0 atom.
>>>> total atoms in file: 4367
>>>> Leap added 1 missing atom according to residue templates:
>>>> 1 Heavy
>>>> Writing pdb file: 1TSRB_R273H+_dry.pdb
>>>> Converting C-terminal residue name to PDB format: CLEU -> LEU
>>>> Total unperturbed charge: -39.000050
>>>> Total perturbed charge: -39.000050
>>>> Quit
>>>>
>>>>
>>>>
>>>> Best regards,
>>>> Mohamed Marzouk Sobeh
>>>> Ph.D student at Life Science and Technology, Tokyo Institute
>>>> of Technology, Tokyo, Japan.
>>>> T.A Physics department,Ain Shams University, Cairo, Egypt.
>>>> Emails:
>>>> mohamed_marzouk.sci.asu.edu.eg <mailto:mohamed_marzouk.sci.asu.edu.eg>
>>>> marzouk.aa.m.titech.ac.jp <mailto:marzouk.aa.m.titech.ac.jp>
>>>> marzouk_biophysics.yahoo.com <mailto:marzouk_biophysics.yahoo.com>
>>>> mohamedmarzoukphysics.gmail.com <mailto:mohamedmarzoukphysics.gmail.com>
>>>>
>>>> Mob. and WhatsApp.:
>>>> +81 070-4070-9549
>>>> +2 01061417414
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>> On Reiwa 3 Nov 27, at 1:34, Dr. Anselm Horn <anselm.horn.fau.de
>>>>> <mailto:anselm.horn.fau.de>> wrote:
>>>>>
>>>>> Mohamed,
>>>>>
>>>>> leap does know the charges of the different histidine species.
>>>>>
>>>>> Although I can see no screenshots in your e-mail (better copy&paste the
>>>>> respective/important parts of the output into your message), chances are
>>>>> that there's an error in your input somewhere, or maybe you inspected
>>>>> the same part of the leap.log file, which is re-used in subsequent leap
>>>>> invocations and further leap output is appended to that file.
>>>>>
>>>>> Good luck,
>>>>>
>>>>> Anselm
>>>>>
>>>>> Bioinformatik | NHR.FAU
>>>>> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
>>>>> Germany
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Am 26.11.2021 um 17:13 schrieb mohamed marzouk:
>>>>>> Hello,
>>>>>> I am trying to study the effect of mutation on my system.
>>>>>> I mutate the Arginine to Histidine
>>>>>> One time, Histidine in form δ-histidine (with residue name in pdb;
>>>>>> HID) , so expected the +ve charge decrease by 1 (of Arg)
>>>>>> The other possibility, Histidine in form protonated form (HIP) ,
>>>>>> so expected the charge not affected ( change positive by positive)
>>>>>> But I found that, both cases give the same total charge before adding
>>>>>> the ions. As in attached screenshots
>>>>>> How can I let tleap now the charge of Histidine ?
>>>>>>
>>>>>> Best regards,
>>>>>> Mohamed Marzouk Sobeh
>>>>>> Ph.D student at Life Science and Technology, Tokyo Institute of
>>>>>> Technology, Tokyo, Japan.
>>>>>> T.A Physics department,Ain Shams University, Cairo, Egypt.
>>>>>> Emails:
>>>>>> mohamed_marzouk.sci.asu.edu.eg <mailto:mohamed_marzouk.sci.asu.edu.eg>
>>>>>> marzouk.aa.m.titech.ac.jp
>>>>>> marzouk_biophysics.yahoo.com
>>>>>> mohamedmarzoukphysics.gmail.com
>>>>>>
>>>>>> Mob. and WhatsApp.:
>>>>>> +81 070-4070-9549
>>>>>> +2 01061417414
>>>>>>
>>>>>>
>>>>>>
>>>>>>
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Received on Fri Nov 26 2021 - 16:30:02 PST
