[gmx-users] Regarding error

[Marzinek, Jan]

________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Seera Suryanarayana [palusoori at gmail.com]
Sent: Friday, May 25, 2012 6:23 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Regarding error

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.


http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database

Jan

Kindly tell me how to over come this error.

Suryanarayana Seera,
PhD student,
Hyderabad,
India.

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