AMBER Archive (2006)

Subject: Re: AMBER: question about REDII

From: Raffaella D'Auria (rdauria_at_uci.edu)
Date: Fri May 12 2006 - 14:12:41 CDT

Dear Francois,

Thanks a lot!!!! Somehow I was misunderstanding the manual so that I was
under the wrong impression that all the atoms with the same name (say C)
must have had also the same number... Your pdb clarified a lot :)

Raffaella.

On Fri, 12 May 2006, FyD wrote:

> > I am quite puzzled by the name assignment in the pdb file that serves as
> > input. In particular suppose I have a series of C atoms which type in
> > amber ff94 is CT, now, since the REDII naming convention all of my C
> > become CT1 (which makes them all equivalent???)? Something about the
> > naming convention must be eluding me... here is the pdb I used as input:
>
> oh oh if it is CH3-CH2-CH2-CH2-OH it should be: see just below
>
> ATOM 1 CT1 1BO 1 3.537 1.423 -0.000 1.00 0.00
> ATOM 2 H1 1BO 1 3.556 1.394 -1.116 1.00 0.00
> ATOM 3 H1 1BO 1 3.581 0.373 0.378 1.00 0.00
> ATOM 4 H1 1BO 1 4.448 1.964 0.354 1.00 0.00
> ATOM 5 CT2 1BO 1 2.293 2.115 0.494 1.00 0.00
> ATOM 6 H2 1BO 1 2.281 3.176 0.124 1.00 0.00
> ATOM 7 H2 1BO 1 2.305 2.156 1.615 1.00 0.00
> ATOM 8 CT3 1BO 1 1.042 1.406 0.027 1.00 0.00
> ATOM 9 H3 1BO 1 1.048 0.345 0.392 1.00 0.00
> ATOM 10 H3 1BO 1 1.016 1.370 -1.093 1.00 0.00
> ATOM 11 CT4 1BO 1 -0.204 2.109 0.534 1.00 0.00
> ATOM 12 H4 1BO 1 -0.249 3.167 0.160 1.00 0.00
> ATOM 13 H4 1BO 1 -0.220 2.115 1.658 1.00 0.00
> ATOM 14 O5 1BO 1 -1.387 1.510 0.039 1.00 0.00
> ATOM 15 H5 1BO 1 -1.367 0.582 0.297 1.00 0.00
>
> Does it help ? Please see also the tutorial in the R.E.D.II manual.
>
> regards, Francois
>
> --
> * F.-Y. Dupradeau *
> DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
> ****
> http://www.u-picardie.fr/labo/lbpd/FyD/
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