Fwd: [gmx-users] Invalid atom number 6415 in indexfile

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 29 01:32:14 CET 2009



Liu Shiyong wrote:
> Hi,
> 
> Thank for your helpful reply.
> 
>  I understand your feeling.   If you have time, please see the following.
> 
>  mdrun has an option to output the final structure(-c). I just knew it 
> after reading your post and checked again  :<
>  Thanks .
> 
>  
>    Firstly, I run a minimized command to get the minimized structure.
> 
>   Secondly, based on the minimized structure, I want to do energy 
> calculation with some user-defined energy groups. I guest I need to run 
> second pdb2gmx.
> 

I don't think you do.  See comments below.

>   The command in the  Step 1:
>      pdb2gmx   -ff G53a6 -f r-l_207655_G53a6.pdb -p r-l_207655_G53a6.top 
> -i r-l_207655_G53a6.posre.itp -o r-l_207655_G53a6.gro > 
> r-l_207655_G53a6.output.pdb2gmx 2>&1 
> 
>   em.mdp
> 
> title               =  
> r-l_207655_G53a6                                                                  
> 
> cpp                 =  
> /usr/bin/cpp                                                                      
> 
> define              =  
> -DFLEX_SPC                                                                        
> 
> constraints         =  
> none                                                                              
> 
> integrator          =  
> l-bfgs                                                                            
> 
> dt                  =  0.002    ; ps 
> !                                                                  
> nsteps              =  
> 10000                                                                             
> 
> nstlist             =  
> 20                                                                                
> 
> ns_type             =  
> simple                                                                            
> 
> rlist               =  
> 1.8                                                                               
> 
> coulombtype         =  
> shift                                                                             
> 
> epsilon_r           =  
> 2.0                                                                               
> 
> rcoulomb            =  
> 1.8                                                                               
> 
> rcoulomb-switch     =  
> 1.7                                                                               
> 
> vdwtype             =  
> shift                                                                             
> 
> rvdw                =  
> 1.5                                                                               
> 
> rvdw_switch         =  
> 1.4                                                                               
> 

These are some bizarre cutoffs for use with 53a6, but perhaps you have your 
reasons...

> pbc                 =  
> no                                                                                
> 
> ;                                                                                                        
> 
> ;       Energy minimizing 
> stuff                                                                          
> 
> ;                                                                                                        
> 
> emtol               =  
> 100.0                                                                             
> 
> emstep              =  0.01      
> 
> 
> grompp -f em.mdp -c r-l_207655_G53a6.gro -p r-l_207655_G53a6.top -po 
> r-l_207655_G53a6.mdout.mdp -o r-l_207655_G53a6.input.tpr > 
> r-l_207655_G53a6.output.grompp 
> 2>&1                                              
> mdrun -nice 0 -v -s r-l_207655_G53a6.input.tpr -o 
> r-l_207655_G53a6.minim_traj.trr -c r-l_207655_G53a6.minimized.pdb -e 
> r-l_207655_G53a6.minim_ener.edr -g r-l_207655_G53a6.emlog.log    > 
> r-l_207655_G53a6.output.mdrun 2>&1
> 
> Now, I get an minimized structure: r-l_207655_G53a6.minimized.pdb
> 
> Then , I remove the Hydrogen atom in r-l_207655_G53a6.minimized.pdb, 
> rename as clean2.pdb
> 

Why are you removing hydrogens?

> 
> *Step 2:*
> Starting structure:  clean2.pdb
> 
> I am trying to calculate the energy according to energy groups
> 
> 
> pdb2gmx   -ff G53a6 -f clean2.pdb -p clean2_0.6.top -i 
> clean2_0.6.posre.itp -o clean2_0.6.gro > clean2_0.6.output.pdb2gmx 2>&1
> 

This is redundant.  In the first pdb2gmx, you processed your structure with the 
53a6 parameter set, adding some polar hydrogens and building a topology.  Then, 
you stripped the hydrogens.  Now you are adding them back.  I see no point in 
all of these iterations.

> make_ndx -f clean2.pdb  -o clean2_0.6.ndx < ./make_ndx.input > 
> clean2_0.6.output.make_ndx 2>&1
> 

Now you're using the original .pdb file (with no hydrogens) to make an index 
group.  *This is where you are probably going wrong* - you are carrying out EM 
steps using a topology that includes H atoms on polar groups, but you are 
constructing index groups that correspond to a structure without H.  Therefore, 
none of the atom numbers will correspond to what you think they are (or want 
them to be).

> em.mdp
> 
> title               =  clean2_0.6
> cpp                 =  /usr/bin/cpp
> integrator          =  cg
> dt                  =  0.002    ; ps !
> nsteps              =  1
> rlist               =  0.55
> nstlist             =  0
> vdwtype             =  Cut-off
> rvdw                =  0.6
> coulombtype         =  shift
> epsilon_r           =  20000
> rcoulomb            =  0.6

Again, really bizarre parameters for use with Gromos96.

> rcoulomb-switch     =  0.55
> energy_grps         =  chB chA
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  100.0
> emstep              =  0.01
> 
> 
> grompp -maxwarn 10 -f em.mdp -c clean2_0.6.gro -n clean2_0.6.ndx -p 
> clean2_0.6.top -o clean2_0.6.input.tpr > clean2_0.6.output.grompp 2>&1
> 
> Then, I got an error msg:
> 
> 
> clean2_0.6.output.grompp
> 
> -------------------------------------------------------
> Program grompp, VERSION 3.3.3
> Source code file: ../../../../src/kernel/grompp.c, line: 307
> 
> Fatal error:
> atoms 4175 and 4183 in charge group 1767 are in different energy groups
> -------------------------------------------------------
> 

Right, because these two atoms were generated from a non-H structure, but you 
are using the .gro and .top files (with H!) as input into grompp.

Here's what I'd recommend:

1. Run pdb2gmx and generate your 53a6 topology.
2. Make index groups from the .gro file generated by pdb2gmx.
3. Don't strip H, just to add them back again :)

Hopefully this makes sense.

-Justin

> "God is a DJ" (Faithless)
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On Wed, Jan 28, 2009 at 12:28 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Liu Shiyong wrote:
> 
>         Hi,
> 
>         Did you get my script ?  
> 
> 
>     As I said just a few days ago, I don't run jobs for people.  I only
>     have allocated time on our University's cluster, which I need for
>     myself.
> 
>     That said, it is also very difficult to go through someone's
>     scripting, laden with variables that mean nothing to anyone else but
>     you, and come up with something meaningful, especially when everyone
>     on this list has their own work to be doing.  As I've said several
>     times, simply posting your command lines with the relevant error
>     message(s) is sufficient.
> 
>     That said, I really have no clue what you're doing with those
>     scripts.  It appears that you are running pdb2gmx, grompp, and
>     mdrun, then using trjconv to dump out the last frame from your
>     energy minimization.  The last step is certainly not necessary;
>     mdrun outputs the lowest-energy coordinates.
> 
>     Then you are running pdb2gmx again, and creating index groups.  I
>     don't understand the purpose of the second pdb2gmx call.
> 
>     The problem you are facing is easily answered with the fact that you
>     simply are again using a structure file that does not have the same
>     number of atoms as the structure you used to create the index file.
>      It appears that your index files simply have two chains of a
>     protein, with the highest atom number being 5966. So of course atom
>     6415 is missing.  The simple fix is to perhaps simplify your naming
>     strategy so you can keep it straight, or instead of scripting
>     everything and potentially making mistakes, to just run the commands
>     interactively until you have everything flowing.
> 
>     -Justin
> 
>         I dump a frame from .trr file.
>         I did not define xtc-grps
>          
>         On Wed, Jan 21, 2009 at 2:00 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> 
> 
> 
>            Liu Shiyong wrote:
> 
>                Hi,
> 
>                 I got an error when do grompp:   The input PDB file
>         comes from
>                the output of GROMACS by trajconv command.
> 
> 
>            <snip>
> 
>                -------------------------------------------------------
>                Program grompp, VERSION 3.3.3
>                Source code file: ../../../../src/kernel/readir.c, line: 838
> 
>                *Fatal error:
>                Invalid atom number 6415 in indexfile*
>                -------------------------------------------------------
> 
> 
>            Instead of screen dumps, it would be a lot more useful to see
>         your
>            .mdp file, as well as the command line (not output from) both
>         grompp
>            and trjconv.  Did you dump the frame from an .xtc file?  What did
>            you specify in xtc-grps?
> 
>            -Justin
> 
>            --    ========================================
> 
>            Justin A. Lemkul
>            Graduate Research Assistant
>            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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> 
> 
> 
>         -- 
>         Shiyong Liu
>         Postdoc
>         center for bioinformatics in the university of kansas
>         Lab: (785)864-1962
>         Email: syliu at ku.edu <mailto:syliu at ku.edu> <mailto:syliu at ku.edu
>         <mailto:syliu at ku.edu>> (shiyongliu at ku.edu
>         <mailto:shiyongliu at ku.edu> <mailto:shiyongliu at ku.edu
>         <mailto:shiyongliu at ku.edu>> or liushiyong at ku.edu
>         <mailto:liushiyong at ku.edu> <mailto:liushiyong at ku.edu
>         <mailto:liushiyong at ku.edu>>)
> 
>         Homepage: http://www.people.ku.edu/~syliu
>         <http://www.people.ku.edu/%7Esyliu>
>         Lab:    http://vakser.bioinformatics.ku.edu/people
>         Phone:      (785) 864-1962
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     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
> 
>     ========================================
> 
> 
> 
> 
> -- 
> Shiyong Liu
> Postdoc
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: syliu at ku.edu <mailto:syliu at ku.edu> (shiyongliu at ku.edu 
> <mailto:shiyongliu at ku.edu> or liushiyong at ku.edu <mailto:liushiyong at ku.edu>)
> 
> Homepage: http://www.people.ku.edu/~syliu 
> <http://www.people.ku.edu/%7Esyliu>
> Lab:    http://vakser.bioinformatics.ku.edu/people
> Phone:      (785) 864-1962
> 
> 
> 
> -- 
> Shiyong Liu
> Postdoc
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: syliu at ku.edu <mailto:syliu at ku.edu> (shiyongliu at ku.edu 
> <mailto:shiyongliu at ku.edu> or liushiyong at ku.edu <mailto:liushiyong at ku.edu>)
> Homepage: http://www.people.ku.edu/~syliu
> Lab:    http://vakser.bioinformatics.ku.edu/people
> Phone:      (785) 864-1962
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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