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
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 1:34, Dr. Anselm Horn <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
>> marzouk.aa.m.titech.ac.jp
>> marzouk_biophysics.yahoo.com
>> mohamedmarzoukphysics.gmail.com
>>
>> Mob. and WhatsApp.:
>> +81 070-4070-9549
>> +2 01061417414
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
>>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 26 2021 - 09:00:02 PST
