Re: psfgen gives wrong psf file

From: ehenriques_at_qui.uc.pt
Date: Wed Oct 20 2010 - 08:51:16 CDT

Indeed, the problem are the two patches being applied by default. One
way to go around this is to declare

PATCHING FIRS NONE LAST NONE

at the end of the topology of your residue.

Hope it helps,

Elsa

Quoting Christian Jorgensen <christian.jorgensen_at_merton.ox.ac.uk>:

> 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
>
>
>
>
>

-- 
Elsa S. Henriques                     e-mail: ehenriques_at_qui.uc.pt
Investigadora Auxiliar
Biologia Estrutural e Computacional (@CNC)
e Grupo de Química Estrutural (@CCC)
Cv15 - RMB Lab
Departamento de Química - Universidade de Coimbra
3004-535 COIMBRA                         Portugal
Tel.: +351 23 9852080 - ext.417
Fax : +351 23 9827703

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