[gmx-users] grompp error! why?

[Justin A. Lemkul]

qing yang wrote:
> Dear gmx-users,
> 
> I am try to simulate the protein-drug, and have used drg.itp from prodrg 
> server2,5(beta). I have also got pro.top from pdb2gmx programs. But when 

PRODRG topologies are often unsatisfactory with respect to charges and charge 
groups assigned.  Looking at the two relevant atom entries you've posted below, 
this is almost certainly the case.  Please see the following:

http://www.gromacs.org/Documentation/How-tos/Parameterization

None of that is related specifically to your error, but I figured I should tell 
you before you waste your time simulating potentially unreliable parameters.

> I issue a grompp command for minimization,grompp gives a fatal error.
> 
> The error is:
> 
>   Error 0 [file "unk.itp",line 4]
> 
> Not enough parameters
> 

So you've pasted some of your topology below, but what exactly is on line 4?

> …..
> 
> Fatal error:
> 
> Bonded/nonbonded atom type '1' not found!

Is this a separate error?  Please post all relevant output, otherwise it gets 
confusing.

> 
> My pro.top file:
> 

This can't be right.  You said pro.top came from pdb2gmx, so there should be 
substantially more in it.  This is not to say that you need to post the entirety 
of your topology, but I doubt what you've shown is correct.  This makes it hard 
to know if you've placed your #include statements appropriately, etc.

>    #include “ffg43a1.itp”
> 
>    #include “unk.itp”
> 
>    [molecules]
> 
>    Protein        1
> 
>    UNK         1
> 
>    SOL          109324
> 
> My drg.itp file:

This snapshot does not provide any really useful information.  Which of these 
lines, if any, is line 4, where grompp starts complaining?  Shouldn't there be a 
[moleculetype] directive at the top of your .itp file, at the very least? 
Providing accurate information will get you to a solution a lot faster :)

-Justin

> 
>   [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>      1       CR1     1  UNK     CBF     1    0.003  12.0110   
>      2        HC     1  UNK     HBF     1    0.035   1.0080   
>    ...............
> [ bonds ]
> ; ai  aj  fu    c0, c1, ...
>    1   2   2    0.109  12300000.0    0.109  12300000.0 ;   CBF  HBF   
>    1   3   2    0.139  10800000.0    0.139  10800000.0 ;   CBF  CBG   
>     .............
> [ pairs ]
> ; ai  aj  fu    c0, c1, ...
>    1   6   1                                           ;   CBF  NBK   
>    1   9   1                                           ;   CBF  CBI   
>    .................
> [ angles ]
> ; ai  aj  ak  fu    c0, c1, ...
>    2   1   3   2    120.0       505.0    120.0       505.0 ;  
>  HBF  CBF  CBG   
>    2   1  13   2    120.0       505.0    120.0       505.0 ;  
>  HBF  CBF  CBE   
>    ................
> [ dihedrals ]
> ; ai  aj  ak  al  fu    c0, c1, m, ...
>   1  13 3   2   2      0.0  167.4        0.0  167.4   ; imp  
>  CBF  CBE  CBG  HBF   
>   3 1   5   4   2      0.0  167.4        0.0  167.4   ; imp  
>  CBG  CBF  CBH  HBG   
> 
> Maybe someone knows what the problem might be?How can I deal with this 
> problem?
> Thanks for your help!
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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