VMD-L Mailing List

From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Jul 25 2007 - 16:37:24 CDT

Somehow i try to figure out it. While renumbering the residues, it make
following residues as consecutive residues.
I think vmd is confused by the CYS-CYS patch. How can I avoid this possible
vmd autopsf patch .

ATOM 2561 N CYS O 349 27.898 -10.507 27.960 1.00 67.61
N
ATOM 2562 CA CYS O 349 28.718 -10.516 29.186 1.00 68.50
C
ATOM 2563 C CYS O 349 27.854 -10.491 30.456 1.00 68.47
C
ATOM 2564 O CYS O 349 28.144 -11.177 31.446 1.00 67.93
O
ATOM 2565 CB CYS O 349 29.703 -9.328 29.212 1.00 69.30
C
ATOM 2566 SG CYS O 349 31.313 -9.594 28.379 1.00 70.96
S
ATOM 2567 N CYS O 358 34.227 -12.221 31.090 1.00 66.54
N
ATOM 2568 CA CYS O 358 33.619 -11.365 30.080 1.00 66.76
C
ATOM 2569 C CYS O 358 34.505 -11.324 28.830 1.00 66.08
C
ATOM 2570 O CYS O 358 35.737 -11.372 28.917 1.00 65.47
O
ATOM 2571 CB CYS O 358 33.389 -9.958 30.668 1.00 67.90
C
ATOM 2572 SG CYS O 358 32.715 -8.670 29.554 1.00 70.30
S

After renumbering it become

ATOM 5182 CB CYS O 341 -9.451 -3.069 32.075 1.00 0.00 P1
C
ATOM 5183 SG CYS O 341 -7.841 -3.335 31.242 1.00 0.00 P1
S
ATOM 5184 N CYS O 341 -11.256 -4.248 30.823 1.00 0.00 P1
N
ATOM 5185 HN CYS O 341 -11.118 -5.033 30.222 0.00 0.00 P1
H
ATOM 5186 CA CYS O 341 -10.436 -4.257 32.049 1.00 0.00 P1
C
ATOM 5187 HA CYS O 341 -9.890 -5.193 32.040 0.00 0.00 P1
H
ATOM 5188 HB1 CYS O 341 -9.950 -2.215 31.564 0.00 0.00 P1
H
ATOM 5189 HB2 CYS O 341 -9.282 -2.742 33.125 0.00 0.00 P1
H
ATOM 5190 C CYS O 341 -11.300 -4.232 33.319 1.00 0.00 P1
C
ATOM 5191 O CYS O 341 -11.010 -4.918 34.309 1.00 0.00 P1
O
ATOM 5192 SG CYS O 342 -6.439 -2.411 32.417 1.00 0.00 P1
S
ATOM 5193 CB CYS O 342 -5.765 -3.699 33.531 1.00 0.00 P1
C
ATOM 5194 N CYS O 342 -4.927 -5.962 33.953 1.00 0.00 P1
N
ATOM 5195 HN CYS O 342 -3.941 -6.088 33.856 0.00 0.00 P1
H
ATOM 5196 CA CYS O 342 -5.535 -5.106 32.943 1.00 0.00 P1
C
ATOM 5197 HA CYS O 342 -6.478 -5.562 32.664 0.00 0.00 P1
H
ATOM 5198 HB1 CYS O 342 -6.492 -3.806 34.367 0.00 0.00 P1
H
ATOM 5199 HB2 CYS O 342 -4.823 -3.323 33.989 0.00 0.00 P1
H
ATOM 5200 C CYS O 342 -4.649 -5.065 31.693 1.00 0.00 P1
C
ATOM 5201 O CYS O 342 -3.417 -5.113 31.780 1.00 0.00 P1
O

Any idea?
thanks a lot in advance

On 7/25/07, snoze pa <snoze.pa_at_gmail.com> wrote:
>
> after renumbering the residue position, i am getting this error
> message/warnings
>
> ENERGY: 16 59623.1590 23155.0444 7366.8470
> 117.0456 -428657.3264 99527.72 0.0000 -238867.5087 -
> 238867.5087 0.0000 11250.8926 16068.9796
> 1510326.2161
>
> BRACKET: 4.92744e-07 70.1241 -2.97522e+08 -4.08148e+06 1.87886e+07
> Warning: Bad global exclusion count, possible error!
> Warning: Increasing cutoff during minimization may avoid this.
> Warning: Bad global bond count!
> Warning: Bad global angle count!
> Warning: Bad global dihedral count!
> Warning: Bad global improper count!
>
> any suggestions
>
> On 7/25/07, snoze pa <snoze.pa_at_gmail.com> wrote:
> >
> > set sel [atomselect top all]
> > $sel set resid [$sel get residue]
> > $sel writepdb renumbered.pdb
> >
> > when i am using above then it is rename the 20A to 20, 20B to 20 and so
> > on.,.. but nothing working!
> >
> >
>