[gmx-users] FMNO topology

David spoel at xray.bmc.uu.se
Thu Jun 16 22:29:57 CEST 2005


On Thu, 2005-06-16 at 16:07 -0400, YOLANDA SMALL wrote:
> 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?
Coordinates are displaced to the wrong column. Try viewing it with
rasmol.

> 
> 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
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the 
> > > www interface or send it to gmx-users-request at gromacs.org.
> > -- 
> > 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > 
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> > 
> > 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++




More information about the gromacs.org_gmx-users mailing list