Please show the residue after you have done loadpdb and then savepdb.
Bill
On 7/7/17 2:20 PM, Rana Rehan Khalid wrote:
> Dear Sir
> here is the part of Histidine that come after H++ . I load the file in the
> xleap program after changing as mentioned below but xleap not add hydrogen
> at that place.
> ATOM 1674 N HIE 105 -3.874 19.310 68.183 1.00
> 0.00 N
> ATOM 1675 H HIE 105 -3.716 20.088 67.557 1.00
> 0.00 H
> ATOM 1676 CA HIE 105 -3.556 19.474 69.579 1.00
> 0.00 C
> ATOM 1677 HA HIE 105 -2.920 18.642 69.884 1.00
> 0.00 H
> ATOM 1678 CB HIE 105 -2.785 20.783 69.894 1.00
> 0.00 C
> ATOM 1679 HB2 HIE 105 -3.283 21.622 69.409 1.00
> 0.00 H
> ATOM 1680 HB3 HIE 105 -2.829 20.946 70.968 1.00
> 0.00 H
> ATOM 1681 CG HIE 105 -1.325 20.762 69.489 1.00
> 0.00 C
> ATOM 1682 ND1 HIE 105 -0.847 21.152 68.250 1.00
> 0.00 N
> ATOM 1683 CE1 HIE 105 0.508 20.984 68.280 1.00
> 0.00 C
> ATOM 1684 HE1 HIE 105 1.161 21.218 67.456 1.00
> 0.00 H
> ATOM 1685 NE2 HIE 105 0.938 20.519 69.440 1.00
> 0.00 N
> ATOM 1686 HE2 HIE 105 1.886 20.296 69.704 1.00
> 0.00 H
> ATOM 1687 CD2 HIE 105 -0.218 20.387 70.199 1.00
> 0.00 C
> ATOM 1688 HD2 HIE 105 -0.249 20.020 71.190 1.00
> 0.00 H
> ATOM 1689 C HIE 105 -4.814 19.391 70.400 1.00
> 0.00 C
> ATOM 1690 O HIE 105 -4.757 18.989 71.559 1.00
> 0.00 O
> I manually change the HIE to HID and remove the ATOM given below
> ATOM 1686 HE2 HIE 105 1.886 20.296 69.704 1.00
> 0.00 H
> and i need hydrogen atom only after ATOM 1682
> to make the file consistent for MCPB.py Kindly guide
>
> Kind Regards
>
>
>
>
>
> On Fri, Jul 7, 2017 at 4:27 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> You edited the pdb to change the residue name, deleted any extra atoms,
>> and made the atom names agree with the names for that residue, and it
>> did not place a new atom for you?
>>
>> Bill
>>
>>
>> On 7/7/17 1:14 PM, Rana Rehan Khalid wrote:
>>> No its not added Sir. Actually I want to convert only one position
>>> hydrogen. remove the epsilon position hydrogen and add it to Delta
>> position
>>> Histidine mean convert HIE TO HID
>>>
>>> On Fri, Jul 7, 2017 at 3:51 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>>
>>>> Have you tried just loadpdb, and see if leap places the H?
>>>>
>>>> Bill
>>>>
>>>>
>>>> On 7/7/17 12:44 PM, Rana Rehan Khalid wrote:
>>>>> Hi Everyone
>>>>>
>>>>> I want to change Histidine protonation state. After H++ the pdb file
>>>> show
>>>>> HIE but i want to change it HID, because in my protein NE position
>> bonded
>>>>> with Fe. While according to HIE that NE protonaed H. I tried to
>> manually
>>>>> change the HIE to HID and remove that NE hydrogen. But I think i have
>> to
>>>>> protonate the ND position Kindly tell me how can i do this?
>>>>>
>>>>> Thanks
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Received on Fri Jul 07 2017 - 15:00:03 PDT
