[gmx-users] FMNO topology

[David]

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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