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