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
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
