________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Seera Suryanarayana [paluso...@gmail.com] Sent: Friday, May 25, 2012 6:23 AM To: gmx-users@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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