[gmx-users] Regarding error

[Justin A. Lemkul]

On 5/25/12 1:23 AM, Seera Suryanarayana wrote:
> Dear all gromacs users,
>
>                                    While i am using the commond" pdb2gmx -f
> 4E82.pdb -o 4E82.gro -p 4E82.top".I am getting the following warnings and errors.
>
>
>
> Warning: Residue EME21 in chain has different type (Other) from starting residue
> ALA1 (Protein).
> Warning: Residue ILE22 in chain has different type (Protein) from starting
> residue ALA1 (Protein).
> Warning: Residue SER23 in chain has different type (Protein) from starting
> residue ALA1 (Protein).
> Warning: Residue GLY24 in chain has different type (Protein) from starting
> residue ALA1 (Protein).
> Warning: Residue ARG25 in chain has different type (Protein) from starting
> residue ALA1 (Protein).
> More than 5 unidentified residues at end of chain - disabling further warnings.
> Identified residue CYS20 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
>                      CYS3    CYS5   CYS10   CYS20   CYS30
>                      SG18    SG36    SG75   SG144   SG228
>      CYS5    SG36   0.834
>     CYS10    SG75   0.936   1.000
>     CYS20   SG144   0.833   0.203   0.935
>     CYS30   SG228   0.856   0.827   0.200   0.788
>     CYS31   SG234   0.202   0.860   0.783   0.820   0.734
> Linking CYS-3 SG-18 and CYS-31 SG-234...
> Linking CYS-5 SG-36 and CYS-20 SG-144...
> Linking CYS-10 SG-75 and CYS-30 SG-228...
> Start terminus ALA-1: NH3+
> End terminus CYS-20: COO-
>
> Fatal error:
> Residue 'EME' not found in residue topology database.
>
> Kindly tell me how to over come this error.
>

Whenever you encounter an error, your first source of information should be 
http://www.gromacs.org/Documentation/Errors.  This error, and most of the others 
you are likely to encounter, have been asked and answered hundreds (if not 
thousands) of times already.  For instance:

http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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