psfgen gives wrong psf file

From: Christian Jorgensen (christian.jorgensen_at_merton.ox.ac.uk)
Date: Wed Oct 20 2010 - 04:32:56 CDT

Hi,
I am trying to generate a PSF file using my psfgen file for ornithine, a 21 atom ligand. I have written a topology file for ornithine, and I have a general topology file top_all27_prot_lipid as well as a PDB file.

Question 1: Do I incorporate the local topology into the general topology file? Which of the two do I reference to in the psfgen?

The PSF/PDB outcome is wrong in that 4 additional atoms are added.

Original PDB file I built:

REMARK original generated coordinate pdb file
ATOM 1 HN1 ORN 1 -1.844 2.841 0.620 1.00 0.00 LIG H
ATOM 2 HN2 ORN 1 -1.012 3.463 0.226 1.00 0.00 LIG H
ATOM 3 N ORN 1 -1.736 2.653 1.709 1.00 0.00 LIG N
ATOM 4 CA ORN 1 -2.840 3.313 0.475 1.00 0.00 LIG C
ATOM 5 HA ORN 1 -1.850 1.459 0.008 1.00 0.00 LIG H
ATOM 6 CT ORN 1 -2.519 0.543 0.446 1.00 0.00 LIG C
ATOM 7 OT1 ORN 1 -0.971 1.258 -0.974 1.00 0.00 LIG O
ATOM 8 OT2 ORN 1 -0.497 2.029 -1.391 1.00 0.00 LIG O
ATOM 9 HO1 ORN 1 -0.927 0.016 -1.770 1.00 0.00 LIG H
ATOM 10 CB ORN 1 -1.908 -0.433 -1.724 1.00 0.00 LIG C
ATOM 11 HB1 ORN 1 0.490 0.595 -3.277 1.00 0.00 LIG H
ATOM 12 HB2 ORN 1 -0.705 -0.609 -3.877 1.00 0.00 LIG H
ATOM 13 CG ORN 1 -1.521 1.393 -3.839 1.00 0.00 LIG C
ATOM 14 HG1 ORN 1 -0.577 0.287 -3.232 1.00 0.00 LIG H
ATOM 15 HG2 ORN 1 0.490 0.595 -3.277 1.00 0.00 LIG H
ATOM 16 CD ORN 1 -0.705 -0.609 -3.877 1.00 0.00 LIG C
ATOM 17 HD1 ORN 1 -1.521 1.393 -3.839 1.00 0.00 LIG H
ATOM 18 HD2 ORN 1 -0.577 0.287 -3.232 1.00 0.00 LIG H
ATOM 19 NE ORN 1 0.490 0.595 -3.277 1.00 0.00 LIG N
ATOM 20 HE1 ORN 1 -0.705 -0.609 -3.877 1.00 0.00 LIG H
ATOM 21 HE2 ORN 1 -1.521 1.393 -3.839 1.00 0.00 LIG H

PDB file produced using psfgen:
REMARK original generated coordinate pdb file
ATOM 1 C ORN 1 0.811 2.971 1.506 0.00 0.00 LIG C !excess
ATOM 2 OT1 ORN 1 0.971 1.258 0.974 1.00 0.00 LIG O
ATOM 3 OT2 ORN 1 0.497 2.029 1.391 1.00 0.00 LIG O
ATOM 4 N ORN 1 1.736 2.653 1.709 1.00 0.00 LIG N
ATOM 5 HT1 ORN 1 0.000 0.000 0.000 -1.00 0.00 LIG H !excess
ATOM 6 HT2 ORN 1 0.000 0.000 0.000 -1.00 0.00 LIG H !excess
ATOM 7 HT3 ORN 1 0.000 0.000 0.000 -1.00 0.00 LIG H !excess
ATOM 8 CA ORN 1 2.840 3.313 0.475 1.00 0.00 LIG C
ATOM 9 HA ORN 1 1.850 1.459 0.008 1.00 0.00 LIG H
ATOM 10 NE ORN 1 0.490 0.595 3.277 1.00 0.00 LIG N
ATOM 11 HE1 ORN 1 0.705 0.609 3.877 1.00 0.00 LIG H
ATOM 12 HE2 ORN 1 1.521 1.393 3.839 1.00 0.00 LIG H
ATOM 13 CD ORN 1 0.705 0.609 3.877 1.00 0.00 LIG C
ATOM 14 HD1 ORN 1 1.521 1.393 3.839 1.00 0.00 LIG H
ATOM 15 HD2 ORN 1 0.577 0.287 3.232 1.00 0.00 LIG H
ATOM 16 CB ORN 1 1.908 0.433 1.724 1.00 0.00 LIG C
ATOM 17 HB1 ORN 1 0.490 0.595 3.277 1.00 0.00 LIG H
ATOM 18 HB2 ORN 1 0.705 0.609 3.877 1.00 0.00 LIG H
ATOM 19 CG ORN 1 1.521 1.393 3.839 1.00 0.00 LIG C
ATOM 20 HG1 ORN 1 0.577 0.287 3.232 1.00 0.00 LIG H
ATOM 21 HG2 ORN 1 0.490 0.595 3.277 1.00 0.00 LIG H
ATOM 22 HN1 ORN 1 1.844 2.841 0.620 1.00 0.00 LIG H
ATOM 23 HN2 ORN 1 1.012 3.463 0.226 1.00 0.00 LIG H
ATOM 24 CT ORN 1 2.519 0.543 0.446 1.00 0.00 LIG C
ATOM 25 HO1 ORN 1 0.927 0.016 1.770 1.00 0.00 LIG H
END

My topology file looks as follows:
RESI ORN 0.00
GROUP
ATOM NE NH3 -0.62
ATOM HE1 HC 0.32 ! HN1
ATOM HE2 HC 0.30 ! |
ATOM CD CT2 -0.18 ! HN2-N
ATOM HD1 HA 0.09 ! | HB1 HG1 HD1 HE1
ATOM HD2 HA 0.09 ! | | | | /
GROUP ! HA-CA--CB--CG--CD--NE
ATOM CB CT2 -0.18 ! | | | | \
ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 HE2
ATOM HB2 HA 0.09 ! OT1=CT
GROUP ! |
ATOM CG CT2 -0.18 ! OT2-HO
ATOM HG1 HA 0.09
ATOM HG2 HA 0.09
GROUP
ATOM N NH3 -0.53
ATOM HN1 HC 0.32
ATOM HN2 HC 0.30
ATOM CA CT1 -0.21
ATOM HA HB 0.09
ATOM CT CD 0.75
ATOM OT1 OB -0.55
ATOM OT2 OH1 -0.61
ATOM HO1 H 0.44
BOND CB CA CG CB CD CG NE CD
BOND N HN1 N HN2 N CA CT CA
BOND CT OT2 OT2 HO CA HA CB HB1 CB HB2
BOND CG HG1 CG HG2 CD HD1 CD HD2
DOUBLE OT1 CT

Question 2: What have I done wrong?
When looking at the PSF file generated it says at the top:

       6 !NTITLE
 REMARKS original generated structure x-plor psf file
 REMARKS 2 patches were applied to the molecule.
 REMARKS topology top_all27_prot_lipid.rtf
 REMARKS segment LIG { first NTER; last CTER; auto angles dihedrals }
 REMARKS defaultpatch NTER LIG:1
 REMARKS defaultpatch CTER LIG:1

2 patches were applied to the molecule. Question 3: Does this help explain the additional atoms?

Thanks

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