[gmx-users] FMNO topology
YOLANDA SMALL
yas102 at psu.edu
Thu Jun 16 22:07:50 CEST 2005
Hi David,
No, there are no tabs in the file, I double checked. Here is the file...does it
work when you try to build the topology?
ATOM 1 FC9A FMNO 1 42.816 36.744 4.975 1.00 20.00
C
ATOM 2 FN10 FMNO 1 42.182 36.840 6.199 1.00 20.00
N
ATOM 3 FC10AFMNO 1 42.668 36.167 7.291 1.00 20.00
C
ATOM 4 FN1 FMNO 1 42.047 36.312 8.437 1.00 20.00
N
ATOM 5 FC2 FMNO 1 42.501 35.638 9.528 1.00 20.00
C
ATOM 6 FO2 FMNO 1 41.915 35.714 10.598 1.00 20.00
O
ATOM 7 FN3 FMNO 1 43.689 34.887 9.438 1.00 20.00
N
ATOM 8 FH3 FMNO 1 44.064 34.514 10.287 1.00 20.00
H
ATOM 9 FC4 FMNO 1 44.369 34.628 8.280 1.00 20.00
C
ATOM 10 FO4 FMNO 1 45.338 33.859 8.233 1.00 20.00
O
ATOM 11 FC4A FMNO 1 43.819 35.318 7.092 1.00 20.00
C
ATOM 12 FN5 FMNO 1 44.402 35.130 5.919 1.00 20.00
N
ATOM 13 FC5A FMNO 1 43.918 35.843 4.858 1.00 20.00
C
ATOM 14 FC6 FMNO 1 44.588 35.762 3.618 1.00 20.00
C
ATOM 15 FC7 FMNO 1 44.239 36.561 2.544 1.00 20.00
C
ATOM 16 FCM7 FMNO 1 45.062 36.474 1.278 1.00 20.00
C
ATOM 17 FC8 FMNO 1 43.150 37.469 2.683 1.00 20.00
C
ATOM 18 FCM8 FMNO 1 42.801 38.463 1.598 1.00 20.00
C
ATOM 19 FC9 FMNO 1 42.430 37.525 3.873 1.00 20.00
C
ATOM 20 FCA FMNO 1 40.978 37.673 6.353 1.00 20.00
C
ATOM 21 FCB FMNO 1 41.297 39.154 6.598 1.00 20.00
C
ATOM 22 FOB FMNO 1 41.998 39.326 7.826 1.00 20.00
O
ATOM 23 FHB FMNO 1 42.835 38.779 7.812 1.00 20.00
H
ATOM 24 FCG FMNO 1 40.023 39.997 6.639 1.00 20.00
C
ATOM 25 FOG FMNO 1 39.289 39.643 7.829 1.00 20.00
O
ATOM 26 FHG FMNO 1 39.864 39.793 8.633 1.00 20.00
H
ATOM 27 FCD FMNO 1 39.143 39.770 5.382 1.00 20.00
C
ATOM 28 FOD FMNO 1 39.877 39.308 4.264 1.00 20.00
O
ATOM 29 FHD FMNO 1 40.386 38.485 4.516 1.00 20.00
H
ATOM 30 FCE FMNO 1 38.340 41.034 5.054 1.00 20.00
C
ATOM 31 FOZ FMNO 1 39.145 42.196 4.963 1.00 20.00
O
ATOM 32 FPH FMNO 1 39.786 42.550 3.438 1.00 20.00
P
ATOM 33 FOH FMNO 1 40.743 41.338 3.184 1.00 20.00
O
ATOM 34 FOT1 FMNO 1 40.559 43.843 3.641 1.00 20.00
O
ATOM 35 FOT2 FMNO 1 38.580 42.633 2.503 1.00 20.00
O
END
On Thu, 16 Jun 2005 19:47:59 +0200, David wrote:
> On Thu, 2005-06-16 at 12:54 -0400, YOLANDA SMALL wrote:
> > Hello,
> >
> > There is some sort of spacing issue that I can't seem to get around. I want
to
> > build the topology for a non-covalently bound flavin group (FMN oxidized
state)
> > with the command:
> > pdb2gmx -f FMNo.pdb -o conf.gro -p topol.top
> >
> > However, I get the following error:
> > Fatal error: Atom FC10 in residue FMNO 1 not found in rtp entry with 36
atoms
> > while sorting atoms
> >
> > Here is the line for that atom from the PDB file
> > ATOM 3 FC10A FMNO 1 42.668 36.167 7.291
> >
> > I tried several spacing options and it seems that pdb2gmx can only read 4
spaces
> > of atom name characters but this atom exists in a 5 character naming
convention
> > in the ffgmx.rtp file. What am I doing wrong?
> Do you have any tabs in the file? Then replace them by spaces.
> >
> > Thanks,
> > Yolanda
> > _______________________________________________
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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