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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>>
>>
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Received on Fri Nov 26 2021 - 09:30:02 PST
