You should be able to click the draw box top right, then click on one
atom and draw to the next before releasing.
If that doesn't work, what kind of hardware/OS are you running on?
It would be faster to
> x = loadpdb the.pdb
> bondbydistance x
> edit x
Then delete the extra bonds, and draw the missing ones.
Bill
On 8/31/17 10:11 AM, Parviz Seifpanahi Shabane wrote:
> Yes, I did, this what I am getting (attached image) after loading TMN.pdb
> to xleap.
>
> On Thu, Aug 31, 2017 at 1:02 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> I only see 1 N atom in the pdb below, and it appears in xleap.
>>
>> I was able to draw bonds between MN and O, N.
>>
>> Did you click on 'Draw' on the top of the xleap editor?
>>
>> Bill
>>
>> On 8/31/17 8:11 AM, Parviz Seifpanahi Shabane wrote:
>>> Dear AMBER users,
>>> I need to add the highly charged ion (-120 e) to my system in certain
>> place
>>> in my PDB file before running simulation, I am following this tutorial:
>>> http://ambermd.org/tutorials/advanced/tutorial1_adv/index.htm
>>> I picked the residue which has the best position (Threonine (Thr)) for my
>>> purpose and created the new residue named TMN by adding the Mn ion to it.
>>> this my TMN.pdb file:
>>>
>>> ATOM 525 N TMN B 96 55.589 87.183 6.224 0.00 0.00
>> N
>>> ATOM 526 CA TMN B 96 56.332 86.013 5.728 0.00 0.00
>> C
>>> ATOM 527 C TMN B 96 57.725 86.436 5.230 0.00 0.00
>> C
>>> ATOM 528 O TMN B 96 57.865 87.357 4.412 0.00 0.00
>> O
>>> ATOM 529 CB TMN B 96 55.580 85.363 4.578 0.00 0.00
>> C
>>> ATOM 530 CG2 TMN B 96 56.358 84.123 3.985 0.00 0.00
>> C
>>> ATOM 531 OG1 TMN B 96 54.305 84.932 5.050 0.00 0.00
>> O
>>> ATOM 908 H TMN B 96 54.624 87.243 5.931 0.00 0.00
>> H
>>> ATOM 909 HA TMN B 96 56.448 85.287 6.533 0.00 0.00
>> H
>>> ATOM 910 HB TMN B 96 55.451 86.086 3.773 0.00 0.00
>> H
>>> ATOM 911 HG21 TMN B 96 55.745 83.227 4.084 0.00 0.00
>> H
>>> ATOM 912 HG22 TMN B 96 56.575 84.299 2.931 0.00 0.00
>> H
>>> ATOM 913 HG23 TMN B 96 57.292 83.985 4.530 0.00 0.00
>> H
>>> ATOM 914 HG1 TMN B 96 54.425 84.288 5.752 0.00 0.00
>> H
>>> ATOM 13626 MN TMN B 96 55.100 90.254 3.700 0.97 51.89
>> MN
>>> problem is in editing step for creating TMN unit and library file I can
>> not
>>> see the Nitrogen (N) atoms (edit TMN.pdb) and I can not draw the bonds
>>> correctly.
>>> any idea?
>>
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>>
>
>
>
>
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Received on Thu Aug 31 2017 - 13:00:04 PDT
