On 9/8/17 5:43 AM, abir paul wrote:
hi,
I am very new to gromacs. I want to see phosphorylation effect on a
protein molecule. So I have phosphorylated my protein in charmm-gui server.
when i tried to generate .gro file by using pdb2gmx command line it gives
me following error :
Fatal error:
Residue 1 named GLY of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
an interaction of type improper in that entry is not found in
the
input file. Perhaps your atom and/or residue naming needs to be
fixed.
How can I fixed this error. please help me.
CHARMM-GUI will build the whole system for you, including generating the
GROMACS topology and input files. There's no need to run anything
through pdb2gmx.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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