On 1/29/13 11:01 AM, az kalsom wrote:
hi,
i am using the following
comamnd
pdb2gmx -ff amber99sb -f proteinamber.pdb -o protei2.pdb -p protein.top
-water spce -ignh
and gets the error
Fatal error:
Residue 2 named GLU of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
how to rename it ?
You may or may not have a naming issue. pdb2gmx is telling you that the
expected atom (CG) is missing from the input file. If you have incomplete
residues, you will need to use some external (non-Gromacs) modeling software to
rebuild the missing elements of the input file.
-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
========================================
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