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

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 14 20:09:26 CEST 2011



ahmet yıldırım wrote:
> Dear Justin,
> 
> Thanks for your valuable helps. How should I rearranged the conf.gro 
> file for 6 EDO ligand?  is the following conf.gro mistake?
> 

Well, it's certainly not working, is it?  You only have one EDO molecule shown 
here.  Is this the only one?  If it is, then you need to build the system to 
reflect what you actually want to do.  No one on this list can tell you that. 
You have to build a starting configuration that fits the goals of your study.

-Justin

> _*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
> 
> 14 Nisan 2011 20:15 tarihinde Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> yazdı:
> 
> 
> 
>     ahmet yıldırım wrote:
> 
>         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"
> 
> 
>     Well, either pdb2gmx built the molecules into your topology or
>     you're #including them in this manner, you should not do both.
> 
>         TRS                 1
>         EDO                 6
> 
> 
>     So this is part of your [molecules] directive?  If you've got six
>     copies of EDO, that's likely where the disconnect comes from - you
>     only had one in your previous coordinate file snippet.
> 
> 
>         Furthermore I added the number of atoms (20) in the second line
>         of the
> 
> 
>     If you have 6 EDO, the necessary addition is more than just 20.
> 
> 
>         .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?
> 
> 
>     Generally H atoms are not present in crystal structures.  If your
>     ligands require certain H atoms, then you must do one of two things:
> 
>     1. Add all the necessary hydrogen atoms to the protein and ligands
>     and run pdb2gmx.
> 
>     2. Have no H atoms present in the initial coordinate file and build
>     suitable .hdb entries for your ligands so they will be constructed
>     from existing atoms.
> 
>     It seems like you're applying several different methods at once.
>      There are protein-ligand tutorials that you may find useful for
>     keeping all of this straight (I recommend my own):
> 
>     http://www.gromacs.org/Documentation/Tutorials#Protein-Ligand_Systems
> 
>     -Justin
> 
>         2011/4/14 Justin A. Lemkul <jalemkul at vt.edu
>         <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>         <mailto: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 <http://vt.edu> <http://vt.edu> | (540)
>         231-9080
> 
>            http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>            ========================================
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> 
> 
> 
>         -- 
>         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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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> 
> 
> 
> -- 
> 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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