[gmx-users] atom type errer

[Justin A. Lemkul]

mohsen ramezanpour wrote:
> Dear All
> 
> I am using protein-drug binding.
> when I am using grompp this error occuring:
> 
> Atomtype CR6 not found
> and
> Atomtype CR5 not found.
> by what can I replace these atom types?

Looks like you're mixing and matching force fields.  Is your drug topology from 
PRODRG?  Please heed the caveats here:

http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips

Atom types CR61 and CR51 are from the deprecated ffgmx (don't use it!), while 
you're probably trying to combine the output with some form of Gromos96. 
Equivalent atom types do exist, but be sure you know what you're doing before 
hacking apart a topology.

-Justin

> this is my drug.itp file:
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>      1       CR61     1  LIG     C11     1    0.021  13.0190  
>      2       CR61     1  LIG     C15     1    0.020  13.0190  
>      3        CB        1  LIG     C17     1    0.040  12.0110  
>      4         O         1  LIG      F1      1   -0.162  18.9984  
>      5       CR61     1  LIG     C16     1    0.021  13.0190  
>      6       CR61     1  LIG     C12     1    0.020  13.0190  
>      7        CB        1  LIG      C6      1    0.040  12.0110  
>      8       CH1       1  LIG      C1       2    0.000  12.0110  
>      9       CH2      1  LIG      C2       2    0.000  14.0270  
>     10       CH2     1  LIG      C5       3    0.120  14.0270  
>     11       CH2     1  LIG      C8       3    0.120  14.0270  
>     12        NL     1  LIG      N1     3    0.675  14.0067  
>     13       CH3     1  LIG     C18     3    0.085  15.0350  
>     14       CH3     1  LIG     C19     4    0.071  15.0350  
>     15         H     1  LIG     HAA     4    0.052   1.0080  
>     16        OS     1  LIG      O1     4   -0.147  15.9994  
>     17       CR51     1  LIG      C7     4   -0.010  13.0190  
>     18        CB     1  LIG      C4     4    0.034  12.0110  
>     19       CR61     1  LIG     C10     5    0.034  13.0190  
>     20        CB     1  LIG      C3     5    0.067  12.0110  
>     21       CR61     1  LIG      C9     5    0.034  13.0190  
>     22       CR61     1  LIG     C13     5    0.034  13.0190  
>     23        CB     1  LIG     C14     5    0.067  12.0110  
>     24        CB     1  LIG     C20     5    0.307  12.0110  
>     25         N     1  LIG      N2     5   -0.543  14.0067  
> 
> thanks in advance
> 

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

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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