[gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

[Justin A. Lemkul]

ahmet yıldırım wrote:
> Dear users,
> 
> pdb2gmx -f xxx.pdb
> water:spc
> forcefield:43a1
> editconf -f conf.gro -bt cubic -d 1.0 -o box.gro
> genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
> *Fatal error:*
> number of coordinates in coordinate file (solvated.gro, 106523) does not 
> match topology (topol.top, 106553)
> I look at gmx-user search. But I dont be able to solved the problem. 
> Then I look at conf.gro and box.gro. I recognised the there is not the 
> TRS ligand in the box.gro file. What reason?
> 

Based on your workflow, it looks as is you never added it in.  If conf.gro came 
from pdb2gmx, did you build .rtp entries for your ligands, or just #include .itp 
files after the fact?  If the latter, then you have to modify the coordinate 
file (conf.gro) to include these molecules.  If you did this but did not 
correctly increment the number of atoms in the second line of the .gro file, 
likely anything with a higher atom number got truncated.  If the conf.gro file 
you show below is indeed what you used, though, I see no reason why this should 
have happened except that perhaps you left out a step you thought you had done 
previously.

The difference in the coordinate file vs. topology is 30 atoms, which is more 
than both of your ligands (20 atoms), so your problem likely lies elsewhere.

-Justin

> Thanks in advance
> 
> _*conf.gro:*_
> MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
>  5354
>     2GLN      N    1   1.458  -1.158   0.739
>     2GLN     H1    2   1.520  -1.083   0.763
> ...
>   485HOH    HW1 5333   0.221  -3.864  -2.291
>   485HOH    HW2 5334   0.303  -3.946  -2.407
>     1EDO  OAB      1   0.625  -3.071  -0.171
>     1EDO  HAA      2   0.698  -3.048  -0.107
>     1EDO  CAA      3   0.596  -3.211  -0.163
>     1EDO  CAC      4   0.486  -3.247  -0.261
>     1EDO  OAD      5   0.365  -3.179  -0.224
>     1EDO  HAB      6   0.292  -3.203  -0.288
>     1TRS  O1       1   1.825  -3.900   0.047
>     1TRS  HAA      2   1.853  -3.860  -0.040
>     1TRS  C1       3   1.712  -3.977   0.028
>     1TRS  C        4   1.659  -4.044   0.150
>     1TRS  C3       5   1.576  -3.946   0.226
>     1TRS  O3       6   1.634  -3.824   0.256
>     1TRS  HAC      7   1.569  -3.768   0.307
>     1TRS  N        8   1.582  -4.159   0.113
>     1TRS  HAE      9   1.547  -4.204   0.195
>     1TRS  HAF     10   1.505  -4.131   0.056
>     1TRS  HAD     11   1.639  -4.223   0.062
>     1TRS  C2      12   1.776  -4.085   0.233
>     1TRS  O2      13   1.887  -4.122   0.160
>     1TRS  HAB     14   1.961  -4.148   0.222
>    8.13100   7.04165  13.54850   0.00000   0.00000  -4.06550   0.00000   
> 0.00000   0.00000
> 
> 
> 
> 
> 
> -- 
> Ahmet YILDIRIM
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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