Re: extra lines in PSF !!!

From: Dan Strahs (dstrahs_at_pace.edu)
Date: Fri Feb 10 2006 - 13:32:07 CST

Georgios:

You haven't supplied enough information, such as your psfgen input, to
make an accurate determination as to what occurred. PSFGEN generates
coordinates of 0.0 when it has to make a guess as to the coordinates
(guesscoord) and it can't determine the location of the atoms from the
constraints available in the input.

What topology file did you use? Where did your coordinates come from? Did
you give psfgen coordinates for all the atoms? What error messages did
psfgen report?

Dan Strahs

On Fri, 10 Feb 2006, Georgios Papadopoulos wrote:

> Dear list,
> does anybody knows a reason why psfgen generated a pdb file
> with 6 additional atom records for URA with 0.000 coordinates?
> Here are the first lines of the pdb and psf files respectively:
>
> PDB
>
> REMARK original generated coordinate pdb file
>
> ATOM 1 N URA 5 0.000 0.000 0.000 -1.00 0.00 A
>
> ATOM 2 HT1 URA 5 0.000 0.000 0.000 -1.00 0.00 A
>
> ATOM 3 HT2 URA 5 0.000 0.000 0.000 -1.00 0.00 A
>
> ATOM 4 HT3 URA 5 0.000 0.000 0.000 -1.00 0.00 A
>
> ATOM 5 CA URA 5 0.000 0.000 0.000 -1.00 0.00 A
>
> ATOM 6 HA URA 5 0.000 0.000 0.000 -1.00 0.00 A
>
> ATOM 7 P URA 5 68.174 2.856 22.013 1.00 0.00 A
>
> ATOM 8 O1P URA 5 67.040 2.445 22.937 1.00 0.00 A
>
> ATOM 9 O2P URA 5 67.797 3.994 21.078 1.00 0.00 A
>
> ATOM 10 O5' URA 5 69.075 2.423 22.019 0.00 0.00 A
>
> ........
>
> PSF
>
> 1 !NTITLE
>
> REMARKS original generated structure x-plor psf file
>
> 87671 !NATOM
>
> 1 A 5 URA N NH3 -0.300000 14.0070 0
>
> 2 A 5 URA HT1 HC 0.330000 1.0080 0
>
> 3 A 5 URA HT2 HC 0.330000 1.0080 0
>
> 4 A 5 URA HT3 HC 0.330000 1.0080 0
>
> 5 A 5 URA CA CT1 0.210000 12.0110 0
>
> 6 A 5 URA HA HB 0.100000 1.0080 0
>
> 7 A 5 URA P P 1.500000 30.9740 0
>
> 8 A 5 URA O1P ON3 -0.780000 15.9994 0
>
> 9 A 5 URA O2P ON3 -0.780000 15.9994 0
>
> 10 A 5 URA O5' ON2 -0.570000 15.9994 0
>
> ......
>
> Bye
>
> G.Papadopoulos
>
>
>

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