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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Received on Thu Aug 31 2017 - 10:30:02 PDT
