AMBER Archive (2004)

Subject: Re: AMBER: Error while protonating a PDB file

From: Madan (amber_list_at_speedpost.net)
Date: Thu Mar 25 2004 - 23:03:56 CST

Dear Case,

Thanks for your help.

I have checked the pdb file and i din't see any duplicate entry of the
coordinates.

I have given the part of the PDB file which has the coordinates of
interest.(I have separated it by giving space for convenience to locate).

I would greatly appreciate if you could tell is there any problem in the
atom nomenclature for the atom that
has these coordinates.

ATOM 323 CE1 HIS 55 54.258 -14.241 38.930 1.00 27.24
   C
ATOM 324 NE2 HIS 55 54.042 -13.115 38.270 1.00 27.33
   N
ATOM 325 N CYS 56 53.298 -10.031 44.210 1.00 20.76
   N
ATOM 326 CA CYS 56 53.695 -9.185 45.336 1.00 18.81
   C
ATOM 327 C CYS 56 52.494 -9.090 46.246 1.00 20.49
   C
ATOM 328 O CYS 56 51.350 -8.952 45.758 1.00 18.36
   O
ATOM 329 CB CYS 56 54.189 -7.782 44.868 1.00 17.13
   C
ATOM 330 SG CYS 56 54.097 -6.431 46.104 1.00 19.10
   S
ATOM 331 N LYS 57 52.764 -9.209 47.546 1.00 13.54
   N
ATOM 332 CA LYS 57 51.728 -9.191 48.547 1.00 13.24
   C
ATOM 333 C LYS 57 51.862 -7.988 49.442 1.00 19.58
   C
ATOM 334 O LYS 57 50.873 -7.515 50.000 1.00 21.28
   O
ATOM 335 CB LYS 57 51.728 -10.468 49.370 1.00 38.70
   C

ATOM 336 CG LYS 57 51.060 -11.635 48.664 1.00 38.79
   C

ATOM 337 N GLU 58 53.083 -7.500 49.611 1.00 18.00
   N
ATOM 338 CA GLU 58 53.278 -6.348 50.484 1.00 17.73
   C
ATOM 339 C GLU 58 54.240 -5.279 50.000 1.00 15.43
   C
ATOM 340 O GLU 58 55.321 -5.585 49.496 1.00 13.30
   O
ATOM 341 CB GLU 58 53.570 -6.749 51.929 1.00 19.29
   C
ATOM 342 CG GLU 58 53.110 -5.618 52.872 1.00 36.44
   C
ATOM 343 CD GLU 58 53.491 -5.819 54.328 1.00 63.45
   C
ATOM 344 OE1 GLU 58 54.492 -6.514 54.619 1.00 65.34
   O
ATOM 345 OE2 GLU 58 52.803 -5.265 55.194 1.00 48.41
   O
ATOM 346 N ILE 59 53.842 -4.023 50.183 1.00 9.53
   N
ATOM 347 CA ILE 59 54.639 -2.876 49.759 1.00 8.65
   C
ATOM 348 C ILE 59 54.955 -1.980 50.947 1.00 13.06
   C
ATOM 349 O ILE 59 54.037 -1.618 51.708 1.00 11.89
   O
ATOM 350 CB ILE 59 53.877 -2.013 48.708 1.00 12.31
   C
ATOM 351 CG1 ILE 59 53.642 -2.810 47.415 1.00 12.23
   C
ATOM 352 CG2 ILE 59 54.697 -0.788 48.341 1.00 10.25
   C
ATOM 353 CD1 ILE 59 52.620 -2.182 46.407 1.00 6.54
   C
ATOM 354 N ILE 60 56.236 -1.617 51.107 1.00 8.38
   N
ATOM 355 CA ILE 60 56.625 -0.752 52.217 1.00 9.66
   C
ATOM 356 C ILE 60 57.212 0.587 51.795 1.00 11.17
   C

Thanks
Mike

On Thu, 25 Mar 2004 17:34:43 -0800, "David A. Case" <case_at_scripps.edu>
said:
> On Thu, Mar 25, 2004, Mike wrote:
> >
> > I got an error while using 'protonate' on a PDB file.
> >
> > The error message is
> >
> > error in finding unit vector:
> > 1 3 51.060 -11.635 48.664 51.060 -11.635 48.664
> > error: case #1.100b, bond r2 has zero length.
> > ip= 2 na= 3 nhyd= ***** protp(1-3,1-4)= 51.21 52.74 52.20
> > 0.00-10.28-10.74-10.19 0.00 50.29 49.58 37.23 0.00
>
> The program thinks you have two atoms in your pdb file that have the
> same coordinates (51.060 -11.635 48.664). You should check to see if
> this
> is so, of if there is any problem in atom nomenclature for the atom that
> has these coordinate or for any nearby atoms. Also, visually check
> the reasonableness of the input coordinates near (51,-11,48).
>
> ...good luck...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
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