Re: VMD-NAMD and PDB element column

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Sun Dec 13 2015 - 12:17:57 CST

I suspect that the corresponding MASS lines in your topology file are
missing the element field, so an empty string over-writes the element
field which the patch is applied. A different topology file that contains
elements was apparently used to build the initial structure.

How exactly did you produce this file?

Jim

On Sat, 12 Dec 2015, Francesco Pietra wrote:

> Hello:
> As far as I can remember, NAMD does not read the element column in the pdb
> file prepared with psfgen.
>
> Even if true, why VMD (1.9.2 Linux in text mode) does not fully build the
> element column of CYS CYSD patched
> ATOM 7589 C HSD A 502 -9.956 31.185 -18.889 1.00 0.00
> PRA C
> ATOM 7590 O HSD A 502 -10.454 31.249 -20.013 1.00 0.00
> PRA O
> ATOM 7591 N CYS A 503 -8.702 30.797 -18.663 1.00 0.00
> PRA N
> ATOM 7592 HN CYS A 503 -8.361 30.759 -17.713 1.00 0.00
> PRA H
> ATOM 7593 CA CYS A 503 -7.905 30.157 -19.699 1.00 0.00
> PRA C
> ATOM 7594 HA CYS A 503 -7.913 30.790 -20.584 1.00 0.00
> PRA H
> ATOM 7595 CB CYS A 503 -6.462 29.977 -19.236 1.00 0.00
> PRA
> ATOM 7596 HB1 CYS A 503 -6.017 30.961 -19.091 1.00 0.00
> PRA
> ATOM 7597 HB2 CYS A 503 -6.440 29.431 -18.291 1.00 0.00
> PRA
> ATOM 7598 SG CYS A 503 -5.529 29.081 -20.452 1.00 0.00
> PRA
> ATOM 7599 C CYS A 503 -8.506 28.785 -19.988 1.00 0.00
> PRA C
> ATOM 7600 O CYS A 503 -8.925 28.083 -19.061 1.00 0.00
> PRA O
>
> and CYM
>
> ATOM 46 N CYM A 4 -36.415 29.381 -46.642 1.00 0.00
> PRA N
> ATOM 47 HN CYM A 4 -35.975 29.520 -45.744 1.00 0.00
> PRA H
> ATOM 48 CA CYM A 4 -35.816 29.990 -47.828 1.00 0.00
> PRA C
> ATOM 49 HA CYM A 4 -36.195 29.506 -48.728 1.00 0.00
> PRA H
> ATOM 50 CB CYM A 4 -36.182 31.474 -47.915 1.00 0.00
> PRA
> ATOM 51 HB1 CYM A 4 -35.625 31.955 -48.719 1.00 0.00
> PRA H
> ATOM 52 HB2 CYM A 4 -37.242 31.549 -48.160 1.00 0.00
> PRA H
> ATOM 53 SG CYM A 4 -35.921 32.354 -46.370 1.00 0.00
> PRA
> ATOM 54 C CYM A 4 -34.294 29.804 -47.881 1.00 0.00
> PRA C
> ATOM 55 O CYM A 4 -33.602 30.512 -48.604 1.00 0.00
> PRA O
>
> (which are graphically perfectly built)?
>
> francesco pietra
>

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