psfgen errors

From: tpreeprem3_at_gatech.edu
Date: Thu Feb 25 2010 - 00:37:46 CST

I have two questions here. Please help.

Question 1)
While trying to generate a psf file of 4 protein (segments A-D), I got one error for each chain. The program implied that it failed to set coordinate for atom O of the last residue in each segment. The program had no problem with the other residues in each chain. What's the problem here? Please help explain.

The error information is as follow:

---------------------------------------------------------------------------
reading coordinates from pdb file proW.pdb for segment A
Warning: failed to set coordinate for atom O PRO:241 A
reading coordinates from pdb file proX.pdb for segment B
Warning: failed to set coordinate for atom O PRO:92 B
reading coordinates from pdb file proY.pdb for segment C
Warning: failed to set coordinate for atom O PRO:63 C
reading coordinates from pdb file proZ.pdb for segment D
Warning: failed to set coordinate for atom O ARG:99 D
------------------------------------------------------------------------

The relevant data in pdb file are as follows. Here, I only show an example from one chain.

..
..
ATOM 11109 O GLY W 238 -24.022 126.622 137.806 1.00 0.79 O
ATOM 11110 N ARG W 239 -22.005 127.550 138.206 1.00 0.79 N
ATOM 11111 CA ARG W 239 -21.796 127.976 136.827 1.00 0.79 C
ATOM 11112 C ARG W 239 -22.941 128.919 136.557 1.00 0.79 C
ATOM 11113 O ARG W 239 -23.933 128.903 137.270 1.00 0.79 O
ATOM 11114 CB ARG W 239 -21.872 126.796 135.865 1.00 57.62 C
ATOM 11115 CG ARG W 239 -20.678 125.868 135.897 1.00 57.62 C
ATOM 11116 CD ARG W 239 -19.575 126.369 134.987 1.00 57.62 C
ATOM 11117 NE ARG W 239 -18.373 125.536 135.036 1.00 57.62 N
ATOM 11118 CZ ARG W 239 -18.329 124.248 134.706 1.00 57.62 C
ATOM 11119 NH1 ARG W 239 -17.177 123.587 134.786 1.00 57.62 N 1+
ATOM 11120 NH2 ARG W 239 -19.434 123.621 134.302 1.00 57.62 N
ATOM 11121 N ALA W 240 -22.825 129.760 135.545 1.00 0.79 N
ATOM 11122 CA ALA W 240 -23.911 130.677 135.247 1.00 0.79 C
ATOM 11123 C ALA W 240 -23.650 131.383 133.943 1.00 0.79 C
ATOM 11124 O ALA W 240 -22.506 131.567 133.551 1.00 0.79 O
ATOM 11125 CB ALA W 240 -24.058 131.690 136.362 1.00 92.85 C
ATOM 11126 N PRO W 241 -24.714 131.791 133.251 1.00 7.39 N
ATOM 11127 CA PRO W 241 -24.585 132.489 131.970 1.00 7.39 C
ATOM 11128 C PRO W 241 -24.502 134.014 132.106 1.00 7.39 C
ATOM 11129 O PRO W 241 -25.461 134.722 131.797 1.00 7.39 O
ATOM 11130 CB PRO W 241 -25.839 132.054 131.244 1.00 13.86 C
ATOM 11131 CG PRO W 241 -26.848 132.066 132.371 1.00 13.86 C
ATOM 11132 CD PRO W 241 -26.111 131.374 133.482 1.00 13.86 C
TER 11132 PRO W 241

----------------------------------------------------------

Question 2)
Even though I specified the pdbalias for nucleotide A U C G, I got the following error while generating a psf file for an RNA structure:

Warning: failed to set coordinate for atom N6 A:85 RNA
Warning: failed to set coordinate for atom O2 C:87 RNA
Warning: failed to set coordinate for atom N4 C:87 RNA
Warning: failed to set coordinate for atom N2 G:89 RNA
Warning: failed to set coordinate for atom O6 G:89 RNA
Warning: failed to set coordinate for atom N7 G:89 RNA
Warning: failed to set coordinate for atom C8 G:89 RNA

....
...

I checked the topology file, there's no need to do the alias for the atoms which show these errors. The same atom in other residues work fine. Also, I noticed that the residue names stayed the same. They should have been changed to the alias and then I would get something like this which is perfectly fine for me.

Warning: poorly guessed coordinate for atom H5' GUA:1 RNA
Warning: poorly guessed coordinate for atom H5'' GUA:1 RNA
Warning: poorly guessed coordinate for atom H4' GUA:1 RNA
Warning: poorly guessed coordinate for atom H1' GUA:1 RNA
Warning: poorly guessed coordinate for atom H8 GUA:1 RNA
Warning: poorly guessed coordinate for atom H2'' GUA:1 RNA
Warning: poorly guessed coordinate for atom H3' GUA:1 RNA
Warning: poorly guessed coordinate for atom H5' URA:2 RNA
Warning: poorly guessed coordinate for atom H5'' URA:2 RNA
Warning: poorly guessed coordinate for atom H4' URA:2 RNA
Warning: poorly guessed coordinate for atom H1' URA:2 RNA
Warning: poorly guessed coordinate for atom H6 URA:2 RNA
Warning: poorly guessed coordinate for atom H5 URA:2 RNA
-------------------------

Could someone please explain what went wrong in the process?
Thank you very much.

Regards,
Thanawadee

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