priya thiyagarajan wrote:
hello sir,
Thanks for your reply..
As you suggest i tried with all available forcefield for my lipopeptide
but i am getting the same error,,
I have posted this link several times before:
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
All the necessary steps are spelled out there. There is no force field that
will contain the residue you seek; you have to add it yourself.
*Processing chain 2 'A' (16 atoms, 1 residues)
Warning: Starting residue BFC1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
The error message tells you exactly what is wrong (in this case, not completing
step #5 in the link above).
8 out of 8 lines of specbond.dat converted successfully
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.5
Source code file: resall.c, line: 581
Fatal error:
Residue 'BFC' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------*
http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database
Also, a result of not completing step #1 in the "adding a residue" link above.
since mine is connected cyclic lipopeptide even i cant try using prodrg
server too.
i dono how to generate my topology file.
pls help me with your answer.
I've tried and at this point am repeating myself. Also note that there are
numerous posts in the list archive about dealing with cyclic peptides (which are
not trivial). I would suggest you search for them. You should also simplify
your system until you understand the workflow. Deal with a custom residue in a
normal linear peptide, then introduce the cyclic peptide and the issues it may
present.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
