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

[ahmet yıldırım]

Dear Justin,

I built .rtp entries for two ligands using (
http://davapc1.bioch.dundee.ac.uk/prodrg/). I added to the topol.top the
following parts:
#include "TRS.itp"
#include "EDO.itp"
TRS                 1
EDO                 6
Furthermore I added the number of atoms (20) in the second line of the .gro
file. may the problem related to pdb file (3NM4.pdb)? Because  -OH groups
seems as -O. isn't it? maybe I'm wrong. What would you recommend?

2011/4/14 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Ahmet YILDIRIM
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110414/e7c6c692/attachment.html>