Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file.

From: Parviz Seifpanahi Shabane <sparviz.vt.edu>
Date: Thu, 31 Aug 2017 13:11:49 -0400

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?
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Parviz Seifpanahi
Ph.D. Candidate
Department of Physics
Virgina Tech, Blacksburg, Va 24061



_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


TMN.png
(image/png attachment: TMN.png)

Received on Thu Aug 31 2017 - 10:30:03 PDT
Custom Search