Bishwajit Das wrote:
when i try to pdb2gmx -f *.pdb -o *_processed.gro -water spce command
in my pdb file then i select AMBER99SB-ILDN force field
(Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) this force field
but a error massage came.
the massage is following:
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Identified residue GLU6 as a starting terminus.
Identified residue GLU6 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus GLU-6: NH3+
End terminus GLU-6: COO-
Checking for duplicate atoms....
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pgutil.c, line: 88
Fatal error:
Atom CG not found in residue seq.nr <http://seq.nr>. 1 while adding atom
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------
then i repair my protein with what if server as instruction given in
gromacs documentation...then i again run the above process but still
showing me a error massage.The massage was His 450 chain is not
complete.How i overcome this problem..please give me a suggestion.
The exact error message, copied and pasted from your terminal along with any
other relevant output, would be useful. As it stands, the output you posted
suggests that you have a single amino acid (since Glu-6 is both the start and
end residue), but this is clearly not the case with the error at hand if
something is wrong with His-450.
No matter the case, the general solution is that the atom naming must match that
of the .rtp entry for the residue being processed. If this is not true, either
you are missing atoms or have a naming mismatch. If the error arises due to a
hydrogen atom, either use -ignh to ignore H atoms in the input and rebuild them,
or fix the naming mismatch.
If you need further help, we need complete information.
-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
========================================
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