VMD-L Mailing List

From: Magnus Andersson (magnus_at_helium.biomol.uci.edu)
Date: Fri Dec 23 2011 - 13:37:19 CST

Hi all,

I'm trying to build NAD using a combination of top_all27_prot_na.rtf and toppar_all27_na_nad_ppi.str. After building the molecule using psfgen, I get some unassigned atoms (ie zeros in coordinate matrix):

This is the psfgen script:

***************************************
package require psfgen
resetpsf
topology top_all27_prot_na.rtf
topology toppar_all27_na_nad_ppi.str

segment NAD {
       pdb NAD.pdb
}
regenerate angles dihedrals
coordpdb NAD.pdb NAD

guesscoord

writepsf output.psf
writepdb output.pdb
***************************************
I have tried both with and without "regenerate..." - doesn't make a difference

This is part of the error message from psfgen:

Warning: failed to set coordinate for atom NC1 NAD:1 NAD
Warning: failed to set coordinate for atom NO4 NAD:1 NAD
Warning: failed to set coordinate for atom NO5 NAD:1 NAD
Warning: failed to set coordinate for atom AO5 NAD:1 NAD
Warning: failed to set coordinate for atom AO4 NAD:1 NAD
Warning: failed to set coordinate for atom AC1 NAD:1 NAD
Warning: failed to set coordinate for atom AC3 NAD:1 NAD
Warning: failed to set coordinate for atom AO3 NAD:1 NAD
Warning: failed to set coordinate for atom NO3 NAD:1 NAD

The output file looks like:

ATOM 1 AC4' NAD C 1 -2.828 -2.919 -82.136 0.00 0.00 NAD C
ATOM 2 AH4' NAD C 1 0.000 0.000 0.000 -1.00 0.00 NAD H
ATOM 3 AO4' NAD C 1 -2.780 -2.019 -81.702 0.00 0.00 NAD O
ATOM 4 AC1' NAD C 1 -2.577 -2.183 -80.362 0.00 0.00 NAD C
ATOM 5 AH1' NAD C 1 0.000 0.000 0.000 -1.00 0.00 NAD H
ATOM 6 AC5 NAD C 1 0.534 -0.260 -80.320 1.00 0.00 NAD C
ATOM 7 AN7 NAD C 1 -0.374 0.719 -80.122 1.00 0.00 NAD N
ATOM 8 AC8 NAD C 1 -1.598 0.143 -80.100 1.00 0.00 NAD C
ATOM 9 AH8 NAD C 1 -2.557 0.660 -79.979 0.00 0.00 NAD H
ATOM 10 AN9 NAD C 1 -1.469 -1.199 -80.267 1.00 0.00 NAD N
ATOM 11 AN1 NAD C 1 2.540 -1.482 -80.631 1.00 0.00 NAD N
ATOM 12 AC2 NAD C 1 1.846 -2.641 -80.723 1.00 0.00 NAD C
ATOM 13 AH2 NAD C 1 2.281 -3.630 -80.890 0.00 0.00 NAD H
ATOM 14 AN3 NAD C 1 0.514 -2.626 -80.606 1.00 0.00 NAD N
ATOM 15 AC4 NAD C 1 -0.159 -1.469 -80.408 1.00 0.00 NAD C
ATOM 16 AC6 NAD C 1 1.919 -0.297 -80.436 1.00 0.00 NAD C
ATOM 17 AN6 NAD C 1 2.682 0.904 -80.344 1.00 0.00 NAD N
ATOM 18 AH61 NAD C 1 3.666 0.812 -80.424 0.00 0.00 NAD H
ATOM 19 AH62 NAD C 1 2.176 1.750 -80.191 0.00 0.00 NAD H
ATOM 20 AC2' NAD C 1 0.000 0.000 0.000 -1.00 0.00 NAD C
ATOM 21 AH2' NAD C 1 0.000 0.000 0.000 -1.00 0.00 NAD H
ATOM 22 AO2' NAD C 1 0.000 0.000 0.000 -1.00 0.00 NAD O
ATOM 23 AH2T NAD C 1 0.000 0.000 0.000 -1.00 0.00 NAD H
ATOM 24 AC3' NAD C 1 0.000 0.000 0.000 -1.00 0.00 NAD C
ATOM 25 AH3' NAD C 1 0.000 0.000 0.000 -1.00 0.00 NAD H
ATOM 26 AO3' NAD C 1 0.000 0.000 0.000 -1.00 0.00 NAD O
ATOM 27 AH3T NAD C 1 0.000 0.000 0.000 -1.00 0.00 NAD H
ATOM 28 AC5' NAD C 1 0.000 0.000 0.000 -1.00 0.00 NAD C
ATOM 29 AH5' NAD C 1 0.000 0.000 0.000 -1.00 0.00 NAD H
ATOM 30 AH5S NAD C 1 0.000 0.000 0.000 -1.00 0.00 NAD H
ATOM 31 AP NAD C 1 -5.271 1.243 -77.311 1.00 0.00 NAD P
ATOM 32 AO1 NAD C 1 -5.510 0.058 -76.367 1.00 0.00 NAD O
ATOM 33 AO2 NAD C 1 -3.526 -4.158 -79.503 1.00 0.00 NAD O
ATOM 34 AO5' NAD C 1 -4.753 2.098 -77.345 0.00 0.00 NAD O

When I look in the toppar_all27_na_nad_ppi.str file, I see problems in the IC section for NAD. All residues that get zero coordinates are associated with a star * instead of a prime '. For ex:

IC AO4' AC3' *AC4 AC5' 1.8868 112.95 -118.10 111.58 1.5491

Here, it should be AC4' instead of *AC4.

I tried to correct for this, but I get the same output - ie zeros for these residues.

Do you know what might be wrong?

This could be charmm related - although I'm not sure, that's why I'm posting this question in this forum.

Thanks!

Magnus Andersson

===================================
Magnus Andersson, PhD
Department of Physiology and Biophysics
University of California, Irvine
Irvine, CA 92697-4560
(949) 824-6993
Fax: (949) 824-8540
===================================